From 39425b3488703ed3724571fa41bbdac101cc43d9 Mon Sep 17 00:00:00 2001 From: julianu Date: Wed, 10 Jul 2024 13:52:55 +0200 Subject: [PATCH 1/4] Fixing a problem with enzyme regexes containing blanks --- pom.xml | 9 ++++++++- .../compiler/parser/MzIdentMLFileParser.java | 3 +++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 6aa694d..1bb23b3 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ de.mpc.pia pia - 1.5.2 + 1.5.3 PIA - Protein Inference Algorithms https://github.com/mpc-bioinformatics/pia @@ -315,6 +315,13 @@ commons-compress ${commons-compress.version} + io.airlift aircompressor diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java index fd01cd5..a78fc07 100755 --- a/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java +++ b/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java @@ -339,6 +339,9 @@ private void checkEnzymeRegEx(Enzyme enzyme) { LOGGER.error("unsupported enzyme: " + param.getName() + " / " + param.getValue()); } } + } else if ((enzyme.getSiteRegexp() != null) && enzyme.getSiteRegexp().contains(" ")) { + // if there are blanks in the regexp, remove them + enzyme.setSiteRegexp(enzyme.getSiteRegexp().replaceAll("\\s", "")); } } From 06116218d31e7dd5b6add0241ca53af77f26969f Mon Sep 17 00:00:00 2001 From: julianu Date: Wed, 10 Jul 2024 13:53:33 +0200 Subject: [PATCH 2/4] updating the shipped psi-ms OBO --- src/main/resources/de/mpc/pia/psi-ms.obo | 9077 +++++++++++++++++++--- 1 file changed, 7898 insertions(+), 1179 deletions(-) diff --git a/src/main/resources/de/mpc/pia/psi-ms.obo b/src/main/resources/de/mpc/pia/psi-ms.obo index 00a1d54..bab5642 100755 --- a/src/main/resources/de/mpc/pia/psi-ms.obo +++ b/src/main/resources/de/mpc/pia/psi-ms.obo @@ -1,14 +1,18 @@ format-version: 1.2 -data-version: 4.0.17 -date: 13:10:2017 11:30 -saved-by: Gerhard Mayer +data-version: 4.1.157 +date: 14:06:2024 13:22 +saved-by: Joshua Klein auto-generated-by: OBO-Edit 2.3.1 -import: http://ontologies.berkeleybop.org/pato.obo -import: http://ontologies.berkeleybop.org/uo.obo +import: http://purl.obolibrary.org/obo/pato.obo +import: http://purl.obolibrary.org/obo/stato.owl default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ +namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ +remark: coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics remark: namespace: MS +remark: namespace: PEFF remark: coverage: Mass spectrometer output files and spectra interpretation +remark: creator: Yasset Perez-Riverol ebi.ac.uk> remark: creator: Matt Chambers vanderbilt.edu> remark: creator: Andreas Bertsch informatik.uni-tuebingen.de> remark: creator: Marius Kallhardt bdal.de> @@ -16,12 +20,18 @@ remark: creator: Eric Deutsch systemsbiology.org> remark: creator: Fredrik Levander immun.lth.se> remark: creator: Pierre-Alain Binz chuv.ch> remark: creator: Gerhard Mayer rub.de> +remark: creator: Joshua Klein bu.edu> +remark: creator: Chris Bielow fu-berlin.de> +remark: creator: Wout Bittremieux health.ucsd.edu> +remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de> +remark: creator: Julian Uszkoreit ruhr-uni-bochum.de> +remark: creator: Mathias Walzer ebi.ac.uk> remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net -remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo -remark: This work is licensed under the Creative Commons Attribution 3.0 Unported License. -remark: To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. +remark: URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo +remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. +remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. ontology: ms [Typedef] @@ -35,6 +45,7 @@ name: has_units [Typedef] id: part_of name: part_of +xref: BFO:0000050 is_transitive: true [Typedef] @@ -45,6 +56,148 @@ name: has_order id: has_domain name: has_domain +[Typedef] +id: has_value_type +name: has value type +def: "'Entity A' has value type 'Entity B', such as xsd:float." [] + +[Typedef] +id: has_structured_representation_in_format +name: has structured representation in format +def: "The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format." [] + +[Typedef] +id: has_metric_category +name: has_metric_category + +[Typedef] +id: has_value_concept +name: has_value_concept + +[Typedef] +id: has_column +name: has_column + +[Typedef] +id: has_optional_column +name: has_optional_column + +[Term] +id: NCIT:C25330 +name: Duration +def: "The period of time during which something continues." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C21514 ! Temporal Qualifier + +[Term] +id: NCIT:C45781 +name: Density +def: "The amount of something per unit size." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C25447 ! Characteristic + +[Term] +id: NCIT:C68811 +name: Cover +def: "Span a region or interval of distance, space or time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C25404 ! Action + +[Term] +id: NCIT:C79083 +name: Outlier +def: "An observation in a data set that is numerically distant from the rest of the data." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C20181 ! Conceptual Entity + +[Term] +id: NCIT:C21514 +name: Temporal Qualifier +def: "Terms used to indicate units of time or other terms associated with time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} +is_a: NCIT:C41009 ! Qualifier + +[Term] +id: NCIT:C41009 +name: Qualifier +def: "A term that helps define and render a concept unique." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Modifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +is_a: NCIT:C20189 ! Property or Attribute + +[Term] +id: NCIT:C25447 +name: Characteristic +def: "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} +synonym: "Characteristics" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Feature" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Features" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +is_a: NCIT:C20189 ! Property or Attribute + +[Term] +id: NCIT:C20189 +name: Property or Attribute +def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} + +[Term] +id: NCIT:C25404 +name: Action +def: "A thing done." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +subset: NCIT:C105763 +synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +synonym: "Generic Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +is_a: NCIT:C43431 ! Activity + +[Term] +id: NCIT:C43431 +name: Activity +def: "An active process; excludes processes and mechanisms which fulfill biological functions." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 3.0.3"} +synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 5.3"} +synonym: "General activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} + +[Term] +id: NCIT:C20181 +name: Conceptual Entity +def: "An organizational header for concepts representing mostly abstract entities." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Conceptual Entity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} + +[Term] +id: NCIT:C16847 +name: Technique +def: "A practiced and regimented skill or series of actions." [] {http://purl.obolibrary.org/obo/NCIT_C16847="NCI"} +is_a: NCIT:C43431 ! Activity + +[Term] +id: NCIT:C19044 +name: Statistical Technique +def: "A method of analyzing or representing statistical data; a procedure for calculating a statistic." [] {http://purl.obolibrary.org/obo/NCIT_C19044="NCI"} +is_a: NCIT:C16847 ! Technique + +[Term] +id: NCIT:C60694 +name: Principal Component +def: "One of the axes representing the projection of varience resulting from principal component analysis." [] {http://purl.obolibrary.org/obo/NCIT_C60694="NCI"} +is_a: NCIT:C19044 ! Statistical Technique + +[Term] +id: NCIT:C25337 +name: Number +def: "A numeral or string of numerals expressing value, quantity, or identification." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C20189 ! Property or Attribute + +[Term] +id: NCIT:C150827 +name: Number of Occurrences +def: "The number of times something happened." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Number of Occurrences" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +is_a: NCIT:C25337 ! Number + [Term] id: MS:0000000 name: Proteomics Standards Initiative Mass Spectrometry Vocabularies @@ -54,15 +207,15 @@ def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS] id: MS:1000001 name: sample number def: "A reference number relevant to the sample under study." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000002 name: sample name def: "A reference string relevant to the sample under study." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000003 @@ -74,25 +227,25 @@ is_a: MS:1000548 ! sample attribute id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000021 ! gram +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000005 name: sample volume def: "Total volume of solution used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000098 ! milliliter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000006 name: sample concentration def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000175 ! gram per liter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000007 @@ -124,8 +277,8 @@ is_obsolete: true id: MS:1000011 name: mass resolution def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000012 @@ -144,28 +297,28 @@ is_obsolete: true id: MS:1000014 name: accuracy def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000015 name: scan rate def: "Rate in Th/sec for scanning analyzers." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units MS:1000807 ! Th/s +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000016 name: scan start time def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute is_a: MS:1002345 ! PSM-level attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000017 @@ -204,25 +357,25 @@ is_a: MS:1000480 ! mass analyzer attribute id: MS:1000022 name: TOF Total Path Length def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000008 ! meter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000023 name: isolation width def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS] comment: This former purgatory term was made obsolete. -xref: value-type:xsd\:float "The allowed value-type for this CV term." relationship: has_units MS:1000040 ! m/z is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000024 name: final MS exponent def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000025 @@ -230,9 +383,9 @@ name: magnetic field strength def: "A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity." [PSI:MS] synonym: "B" EXACT [] synonym: "Magnetic Field" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000228 ! tesla +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000026 @@ -250,17 +403,17 @@ relationship: part_of MS:1000453 ! detector id: MS:1000028 name: detector resolution def: "The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000481 ! detector attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000029 name: sampling frequency def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] synonym: "ADC Sampling Frequency" NARROW [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000481 ! detector attribute relationship: has_units UO:0000106 ! hertz +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000030 @@ -279,13 +432,13 @@ relationship: part_of MS:1000463 ! instrument id: MS:1000032 name: customization def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000496 ! instrument attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000033 name: deisotoping -def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] +def: "The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] @@ -340,16 +493,16 @@ is_a: UO:0000000 ! unit [Term] id: MS:1000041 name: charge state -def: "The charge state of the ion, single or multiple and positive or negatively charged." [PSI:MS] +def: "Number of net charges, positive or negative, on an ion." [PSI:MS] synonym: "z" EXACT [] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute +is_a: MS:1000507 ! ion property +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000042 name: peak intensity def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak @@ -357,6 +510,7 @@ relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: part_of MS:1000231 ! peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000043 @@ -375,9 +529,9 @@ relationship: part_of MS:1000456 ! precursor activation id: MS:1000045 name: collision energy def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000046 @@ -427,8 +581,8 @@ is_a: MS:1000003 ! sample state id: MS:1000053 name: sample batch def: "Sample batch lot identifier." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000054 @@ -948,8 +1102,8 @@ is_a: MS:1000043 ! intensity unit id: MS:1000132 name: percent of base peak def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000043 ! intensity unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000133 @@ -986,16 +1140,15 @@ id: MS:1000137 name: electron volt def: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266). -synonym: "eV" EXACT [] is_obsolete: true [Term] id: MS:1000138 name: normalized collision energy def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000139 @@ -1401,7 +1554,8 @@ def: "The operation of a mass spectrometer in which the intensities of several s synonym: "MIM" RELATED [] synonym: "Multiple Ion Monitoring" EXACT [] synonym: "SIM" EXACT [] -is_a: MS:1000596 ! measurement method +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1000206 @@ -1410,35 +1564,36 @@ def: "Data acquired from specific product ions corresponding to m/z selected pre synonym: "MRM" RELATED [] synonym: "Multiple Reaction Monitoring" RELATED [] synonym: "SRM" EXACT [] -is_a: MS:1000596 ! measurement method +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1000207 name: accurate mass def: "OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000208 name: average mass def: "OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000209 name: appearance energy def: "OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS] synonym: "AE" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000266 ! electronvolt is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000210 @@ -1451,16 +1606,14 @@ is_a: MS:1000231 ! peak id: MS:1000211 name: OBSOLETE charge number def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS] -synonym: "z" EXACT [] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_obsolete: true +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000212 name: dalton def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221). -synonym: "Da" EXACT [] is_obsolete: true [Term] @@ -1469,8 +1622,8 @@ name: electron affinity def: "OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. synonym: "EA" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000214 @@ -1483,10 +1636,10 @@ is_obsolete: true id: MS:1000215 name: exact mass def: "OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000216 @@ -1507,8 +1660,8 @@ id: MS:1000218 name: ionization efficiency def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000219 @@ -1516,9 +1669,9 @@ name: ionization energy def: "OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS] synonym: "IE" EXACT [] comment: This child of the former purgatory term ion attribute was made obsolete. -xref: value-type:xsd\:float "The allowed value-type for this CV term." relationship: has_units UO:0000266 ! electronvolt is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000220 @@ -1538,36 +1691,35 @@ is_a: MS:1000597 ! ion optics type id: MS:1000222 name: mass defect def: "OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000223 name: mass number def: "OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. is_obsolete: true +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000224 name: molecular mass -def: "OBSOLETE The mass of one mole of a molecular substance (6.022 1415(10) x 10^23 molecules)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -comment: This child of the former purgatory term ion attribute was made obsolete. +def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass] +is_a: MS:1000861 ! molecular entity property relationship: has_units UO:0000002 ! mass unit -is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000225 name: monoisotopic mass def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000226 @@ -1595,10 +1747,10 @@ is_obsolete: true id: MS:1000229 name: nominal mass def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000230 @@ -1626,31 +1778,30 @@ name: proton affinity def: "OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS] synonym: "PA" EXACT [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000234 name: mass resolving power def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS] comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800). -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000235 name: total ion current chromatogram -def: "Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time." [PSI:MS] +def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS] synonym: "TIC chromatogram" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000810 ! mass chromatogram +is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1000236 name: transmission def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000496 ! instrument attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000237 @@ -1842,7 +1993,7 @@ id: MS:1000262 name: infrared multiphoton dissociation def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS] synonym: "IRMPD" EXACT [] -is_a: MS:1000044 ! dissociation method +is_a: MS:1000435 ! photodissociation [Term] id: MS:1000263 @@ -1870,12 +2021,12 @@ is_obsolete: true [Term] id: MS:1000266 name: Laser Desorption -alt_id: MS:1000393 def: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS] comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393). synonym: "Laser Ionization MERGE" EXACT [] synonym: "LD" EXACT [] is_obsolete: true +replaced_by: MS:1000393 [Term] id: MS:1000267 @@ -2015,8 +2166,8 @@ id: MS:1000285 name: total ion current def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS] synonym: "TIC" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000286 @@ -2147,9 +2298,9 @@ is_obsolete: true id: MS:1000304 name: accelerating voltage def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000305 @@ -2175,9 +2326,9 @@ is_a: MS:1000597 ! ion optics type id: MS:1000308 name: electric field strength def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000268 ! volt per meter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000309 @@ -2270,7 +2421,6 @@ id: MS:1000322 name: charge inversion mass spectrum def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000323 @@ -2295,7 +2445,6 @@ name: constant neutral gain spectrum def: "A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell." [PSI:MS] synonym: "constant neutral mass gain spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000326 @@ -2303,7 +2452,6 @@ name: constant neutral loss spectrum def: "A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] synonym: "constant neutral mass loss spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000327 @@ -2370,9 +2518,9 @@ is_obsolete: true [Term] id: MS:1000336 name: neutral loss -def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] is_a: MS:1001055 ! modification parameters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000337 @@ -2409,7 +2557,6 @@ id: MS:1000341 name: precursor ion spectrum def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000342 @@ -2425,7 +2572,6 @@ name: product ion spectrum def: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS] comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content is_obsolete: true [Term] @@ -2489,7 +2635,7 @@ is_obsolete: true id: MS:1000353 name: adduct ion def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] -is_a: MS:1002806 ! ion +is_a: MS:1003055 ! adduct [Term] id: MS:1000354 @@ -2751,8 +2897,8 @@ is_obsolete: true id: MS:1000392 name: ionization efficiency def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000393 @@ -2760,6 +2906,12 @@ name: laser desorption ionization def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS] is_a: MS:1000247 ! desorption ionization +[Term] +id: MS:1000394 +name: no sequence database +def: "No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing." [PSI:PI] +is_a: MS:1001347 ! database file format + [Term] id: MS:1000395 name: liquid secondary ionization @@ -2871,8 +3023,8 @@ is_obsolete: true id: MS:1000412 name: buffer gas def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000413 @@ -2920,8 +3072,8 @@ is_obsolete: true id: MS:1000419 name: collision gas def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000420 @@ -3048,7 +3200,7 @@ is_obsolete: true id: MS:1000437 name: ion reaction def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS] -comment: This child of the former purgatory term ion? was made obsolete. +comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] @@ -3081,7 +3233,7 @@ relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000442 name: spectrum -def: "A mass spectrum is an intensity vs m/z (mass-to-charge ratio) plot representing a chemical analysis." [PSI:MS] +def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] @@ -3364,9 +3516,9 @@ is_a: MS:1000057 ! electrospray inlet id: MS:1000486 name: source potential def: "Potential difference at the MS source in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000487 @@ -3433,9 +3585,9 @@ relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000497 name: zoom scan -def: "Special scan mode, where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS] +def: "Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS] synonym: "enhanced resolution scan" EXACT [] -is_a: MS:1000499 ! spectrum attribute +is_a: MS:1000503 ! scan attribute [Term] id: MS:1000498 @@ -3447,8 +3599,7 @@ is_obsolete: true [Term] id: MS:1000499 name: spectrum attribute -def: "Spectrum properties that are associated with a value." [PSI:MS] -is_a: MS:1000547 ! object attribute +def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] @@ -3456,33 +3607,33 @@ id: MS:1000500 name: scan window upper limit def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS] synonym: "mzRangeStop" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000501 name: scan window lower limit def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS] synonym: "mzRangeStart" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000502 name: dwell time def: "The time spent gathering data across a peak." [PSI:MS] synonym: "Scan Duration" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000503 name: scan attribute -def: "Scan properties that are associated with a value." [PSI:MS] +def: "Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan @@ -3490,50 +3641,49 @@ relationship: part_of MS:1000441 ! scan id: MS:1000504 name: base peak m/z def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute +is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000505 name: base peak intensity def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute +is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000506 name: ion role def: "OBSOLETE Ion Role." [PSI:MS] -comment: This child of the former purgatory term ion? was made obsolete. +comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] id: MS:1000507 -name: ion attribute -def: "OBSOLETE Ion properties that are associated with a value." [PSI:MS] -comment: This child of the former purgatory term ion? was made obsolete. -is_obsolete: true +name: ion property +def: "Nonphysical characteristic attributed to an ion." [PSI:MS] +relationship: part_of MS:1002806 ! ion [Term] id: MS:1000508 name: ion chemical type def: "OBSOLETE Ion Type." [PSI:MS] -comment: This child of the former purgatory term ion? was made obsolete. +comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] id: MS:1000509 name: activation energy def: "Activation Energy." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000510 @@ -3544,16 +3694,16 @@ relationship: part_of MS:1000456 ! precursor activation [Term] id: MS:1000511 name: ms level -def: "Stages of ms achieved in a multi stage mass spectrometry experiment." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." +def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS] is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000512 name: filter string def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000513 @@ -3641,7 +3791,7 @@ is_a: MS:1000518 ! binary data type id: MS:1000524 name: data file content def: "Describes the data content on the file." [PSI:MS] -relationship: part_of MS:1000577 ! raw data file +relationship: part_of MS:1000577 ! source data file [Term] id: MS:1000525 @@ -3659,26 +3809,26 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1000527 name: highest observed m/z def: "Highest m/z value observed in the m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute is_a: MS:1000808 ! chromatogram attribute +is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000528 name: lowest observed m/z def: "Lowest m/z value observed in the m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute is_a: MS:1000808 ! chromatogram attribute +is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000529 name: instrument serial number def: "Serial Number of the instrument." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000496 ! instrument attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000530 @@ -3899,7 +4049,7 @@ is_a: MS:1001459 ! file format id: MS:1000561 name: data file checksum type def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS] -relationship: part_of MS:1000577 ! raw data file +relationship: part_of MS:1000577 ! source data file [Term] id: MS:1000562 @@ -3940,16 +4090,16 @@ is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000568 name: MD5 -def: "MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] is_a: MS:1000561 ! data file checksum type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000569 name: SHA-1 -def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [PSI:MS] is_a: MS:1000561 ! data file checksum type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000570 @@ -3996,10 +4146,11 @@ is_a: MS:1000572 ! binary data compression type [Term] id: MS:1000577 -name: raw data file -def: "Describes the type of file and its content." [PSI:MS] +name: source data file +def: "Data file from which an entity is sourced." [PSI:MS] synonym: "source file" EXACT [] relationship: part_of MS:1001458 ! spectrum generation information +is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1000578 @@ -4016,7 +4167,6 @@ synonym: "Q1 spectrum" EXACT [] synonym: "Q3 spectrum" EXACT [] synonym: "Single-Stage Mass Spectrometry" EXACT [] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000580 @@ -4026,14 +4176,12 @@ synonym: "multiple-stage mass spectrometry spectrum" EXACT [] synonym: "nth generation product ion spectrum" EXACT [] synonym: "product ion spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000581 name: CRM spectrum def: "Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000582 @@ -4043,7 +4191,6 @@ synonym: "MIM spectrum" EXACT [] synonym: "multiple ion monitoring spectrum" EXACT [] synonym: "selected ion monitoring spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000583 @@ -4053,7 +4200,6 @@ synonym: "MRM spectrum" EXACT [] synonym: "multiple reaction monitoring spectrum" EXACT [] synonym: "selected reaction monitoring spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum -is_a: MS:1000524 ! data file content [Term] id: MS:1000584 @@ -4072,36 +4218,36 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom id: MS:1000586 name: contact name def: "Name of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000587 name: contact address def: "Postal address of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000588 name: contact URL def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000589 name: contact email def: "Email address of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000590 name: contact affiliation def: "Home institution of the contact person." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000591 @@ -4153,7 +4299,7 @@ is_a: MS:1000462 ! ion optics [Term] id: MS:1000598 name: electron transfer dissociation -def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them." [PSI:MS] +def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions." [DOI:10.1073/pnas.0402700101, PMID:15210983, PSI:MS] synonym: "ETD" EXACT [] is_a: MS:1000044 ! dissociation method @@ -4269,8 +4415,8 @@ is_a: MS:1001457 ! data processing software id: MS:1000616 name: preset scan configuration def: "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000617 @@ -4285,19 +4431,19 @@ relationship: has_units UO:0000018 ! nanometer id: MS:1000618 name: highest observed wavelength def: "Highest wavelength observed in an EMR spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute +is_a: MS:1003058 ! spectrum property is_a: MS:1000808 ! chromatogram attribute relationship: has_units UO:0000018 ! nanometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000619 name: lowest observed wavelength def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute +is_a: MS:1003058 ! spectrum property is_a: MS:1000808 ! chromatogram attribute relationship: has_units UO:0000018 ! nanometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000620 @@ -4337,41 +4483,39 @@ is_a: MS:1000026 ! detector type [Term] id: MS:1000625 name: chromatogram -def: "The representation of detector response versus time." [PSI:MS] +def: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000626 name: chromatogram type -def: "Broad category or type of a chromatogram." [PSI:MS] +def: "Type of chromatogram measurement being represented." [PSI:MS] relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000627 name: selected ion current chromatogram -def: "Chromatogram created by creating an array of the measurements of a specific single ion current at each time point." [PSI:MS] +def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS] synonym: "SIC chromatogram" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000810 ! mass chromatogram +is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1000628 name: basepeak chromatogram -def: "Chromatogram created by creating an array of the most intense peaks at each time point." [PSI:MS] -is_a: MS:1000524 ! data file content -is_a: MS:1000810 ! mass chromatogram +def: "Representation of an array of the most intense peaks versus time." [PSI:MS] +is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1000629 name: low intensity threshold def: "Threshold below which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000630 @@ -4383,13 +4527,13 @@ relationship: part_of MS:1001458 ! spectrum generation information id: MS:1000631 name: high intensity threshold def: "Threshold above which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000632 @@ -4401,8 +4545,8 @@ is_a: MS:1000126 ! Waters instrument model id: MS:1000633 name: possible charge state def: "A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000634 @@ -5147,9 +5291,9 @@ is_a: MS:1000494 ! Thermo Scientific instrument model id: MS:1000744 name: selected ion m/z def: "Mass-to-charge ratio of an selected ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000745 @@ -5167,8 +5311,8 @@ is_a: MS:1001486 ! data filtering id: MS:1000747 name: completion time def: "The time that a data processing action was finished." [PSI:MS] -xref: value-type:xsd\:date "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter +relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term [Term] id: MS:1000748 @@ -5298,7 +5442,7 @@ id: MS:1000767 name: native spectrum identifier format def: "Describes how the native spectrum identifiers are formated." [PSI:MS] synonym: "nativeID format" EXACT [] -relationship: part_of MS:1000577 ! raw data file +relationship: part_of MS:1000577 ! source data file [Term] id: MS:1000768 @@ -5427,45 +5571,43 @@ xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000522 "64-bit integer" xref: binary-data-type:MS\:1000523 "64-bit float" xref: binary-data-type:MS\:1001479 "null-terminated ASCII string" -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000513 ! binary data array +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000787 name: inclusive low intensity threshold def: "Threshold at or below which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000788 name: inclusive high intensity threshold def: "Threshold at or above which some action is taken." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000789 name: enhanced multiply charged spectrum def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS] -is_a: MS:1000524 ! data file content is_a: MS:1000579 ! MS1 spectrum [Term] id: MS:1000790 name: time-delayed fragmentation spectrum def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS] -is_a: MS:1000524 ! data file content is_a: MS:1000580 ! MSn spectrum [Term] @@ -5487,20 +5629,20 @@ id: MS:1000793 name: isolation window upper limit def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS] comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000794 name: isolation window lower limit def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS] comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000795 @@ -5511,43 +5653,43 @@ is_a: MS:1000570 ! spectra combination [Term] id: MS:1000796 name: spectrum title -def: "A free-form text title describing a spectrum." [PSI:MS] +def: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS] comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000797 name: peak list scans def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000798 name: peak list raw scans def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000499 ! spectrum attribute is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000799 name: custom unreleased software tool def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000531 ! software +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000800 name: mass resolving power def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000801 @@ -5567,9 +5709,9 @@ is_a: MS:1000035 ! peak picking id: MS:1000803 name: analyzer scan offset def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000804 @@ -5611,20 +5753,20 @@ id: MS:1000809 name: chromatogram title def: "A free-form text title describing a chromatogram." [PSI:MS] comment: This is the preferred storage place for the spectrum title. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000808 ! chromatogram attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000810 -name: mass chromatogram -def: "A plot of the relative abundance of a beam or other collection of ions as a function of the retention time." [PSI:MS] +name: ion current chromatogram +def: "Representation of the current of ions versus time." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000811 name: electromagnetic radiation chromatogram -def: "The measurement of electromagnetic properties as a function of the retention time." [PSI:MS] +def: "Representation of electromagnetic properties versus time." [PSI:MS] synonym: "EMR radiation chromatogram" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type @@ -5632,15 +5774,13 @@ is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000812 name: absorption chromatogram -def: "The measurement of light absorbed by the sample as a function of the retention time." [PSI:MS] -is_a: MS:1000524 ! data file content +def: "Representation of light absorbed by the sample versus time." [PSI:MS] is_a: MS:1000811 ! electromagnetic radiation chromatogram [Term] id: MS:1000813 name: emission chromatogram -def: "The measurement of light emitted by the sample as a function of the retention time." [PSI:MS] -is_a: MS:1000524 ! data file content +def: "Representation of light emitted by the sample versus time." [PSI:MS] is_a: MS:1000811 ! electromagnetic radiation chromatogram [Term] @@ -5688,6 +5828,7 @@ def: "A data array of flow rate measurements." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000271 ! microliters per minute [Term] id: MS:1000821 @@ -5729,34 +5870,44 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1000826 name: elution time def: "The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000827 name: isolation window target m/z def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000828 name: isolation window lower offset def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000829 name: isolation window upper offset def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1000830 +name: precision +def: "Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation." [PSI:MS] +comment: See MS:1000014 for the related term of accuracy. +is_a: MS:1000480 ! mass analyzer attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000831 @@ -5781,16 +5932,16 @@ relationship: part_of MS:1000832 ! MALDI matrix application id: MS:1000834 name: matrix solution def: "Describes the chemical solution used as matrix." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000832 ! MALDI matrix application +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000835 name: matrix solution concentration def: "Concentration of the chemical solution used as matrix." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000832 ! MALDI matrix application relationship: has_units UO:0000175 ! gram per liter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000836 @@ -5840,58 +5991,58 @@ id: MS:1000843 name: wavelength def: "OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS] comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242). -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000018 ! nanometer is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000844 name: focus diameter x def: "Describes the diameter of the laser beam in x direction." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000017 ! micrometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000845 name: focus diameter y def: "Describes the diameter of the laser beam in y direction." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000017 ! micrometer +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000846 name: pulse energy def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000112 ! joule +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000847 name: pulse duration def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000150 ! nanosecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000848 name: attenuation def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000849 name: impact angle def: "Describes the angle between the laser beam and the sample target." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000185 ! degree +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000850 @@ -5945,84 +6096,84 @@ is_a: MS:1000547 ! object attribute id: MS:1000858 name: fraction identifier def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000857 ! run attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000859 name: molecule -def: "A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction." [PSI:MS] -relationship: part_of MS:1000881 ! chemical compound +def: "Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule] +is_a: MS:1000881 ! molecular entity [Term] id: MS:1000860 name: peptide -def: "A compound of low molecular weight that is composed of two or more amino acids." [PSI:MS] -is_a: MS:1000881 ! chemical compound +def: "A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS] +is_a: MS:1000859 ! molecule [Term] id: MS:1000861 -name: chemical compound attribute -def: "A describable property of a chemical compound." [PSI:MS] -relationship: part_of MS:1000881 ! chemical compound +name: molecular entity property +def: "A physical characteristic of a molecular entity." [PSI:MS] +relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1000862 name: isoelectric point def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS] synonym: "pI" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000861 ! chemical compound attribute +is_a: MS:1000861 ! molecular entity property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000863 name: predicted isoelectric point def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS] synonym: "predicted pI" EXACT [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000862 ! isoelectric point +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000864 -name: chemical compound formula -def: "A combination of symbols used to express the chemical composition of a compound." [PSI:MS] -relationship: part_of MS:1000881 ! chemical compound +name: chemical formula +def: "A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846] +is_a: MS:1003033 ! molecular entity attribute [Term] id: MS:1000865 name: empirical formula def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical compound formula +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000866 name: molecular formula def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical compound formula +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000867 name: structural formula def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical compound formula +is_a: MS:1000864 ! chemical formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000868 name: SMILES string -def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000864 ! chemical compound formula +def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301] +is_a: MS:1000867 ! structural formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000869 name: collision gas pressure def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000110 ! pascal +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000870 @@ -6060,169 +6211,172 @@ is_a: MS:1000873 ! peptide attribute calculation software id: MS:1000875 name: declustering potential def: "Potential difference between the orifice and the skimmer in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000876 name: cone voltage def: "Potential difference between the sampling cone/orifice in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000877 name: tube lens voltage def: "Potential difference setting of the tube lens in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000878 name: external reference identifier def: "An identifier/accession number to an external reference database." [PSI:MS] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies +is_a: MS:1002840 ! external reference data [Term] id: MS:1000879 name: PubMed identifier def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1000880 name: interchannel delay def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000881 -name: chemical compound -def: "A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight." [PSI:MS] +name: molecular entity +def: "Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [https://en.wikipedia.org/wiki/Molecular_entity] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1000882 name: protein -def: "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein." [PSI:MS] -is_a: MS:1000881 ! chemical compound +def: "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene." [PSI:MS] +is_a: MS:1000859 ! molecule [Term] id: MS:1000883 name: protein short name def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000884 name: protein attribute -def: "An nonphysical attribute describing a specific protein." [PSI:MS] +def: "An nonphysical characterstic attributed to a specific protein." [PSI:MS] relationship: part_of MS:1000882 ! protein is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1000885 name: protein accession -def: "Accession number for a specific protein in a database." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "Identifier for a specific protein in a database." [PSI:MS] is_a: MS:1000884 ! protein attribute +is_a: MS:1003046 ! peptide-to-protein mapping attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000886 name: protein name def: "A long name describing the function of the protein." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000887 name: peptide attribute -def: "A nonphysical attribute that can be used to describe a peptide." [PSI:MS] +def: "Nonphysical characteristic attributed to a peptide." [PSI:MS] relationship: part_of MS:1000860 ! peptide [Term] id: MS:1000888 -name: unmodified peptide sequence -def: "A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000887 ! peptide attribute +name: stripped peptide sequence +def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS] +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000889 -name: modified peptide sequence -def: "A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid modifications that are present." [PSI:MS] +name: peptidoform sequence +def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS] comment: Make it more general as there are actually many other ways to display a modified peptide sequence. -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000887 ! peptide attribute +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000890 -name: peptide labeling state +name: peptidoform labeling state def: "A state description of how a peptide might be isotopically or isobarically labelled." [PSI:MS] -is_a: MS:1000887 ! peptide attribute +is_a: MS:1003050 ! peptidoform attribute [Term] id: MS:1000891 -name: heavy labeled peptide +name: heavy labeled peptidoform def: "A peptide that has been created or labelled with some heavier-than-usual isotopes." [PSI:MS] -is_a: MS:1000890 ! peptide labeling state +is_a: MS:1000890 ! peptidoform labeling state [Term] id: MS:1000892 -name: unlabeled peptide +name: unlabeled peptidoform def: "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:MS] synonym: "light labeled peptide" EXACT [] -is_a: MS:1000890 ! peptide labeling state +is_a: MS:1000890 ! peptidoform labeling state [Term] id: MS:1000893 -name: peptide group label +name: peptidoform group label def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000887 ! peptide attribute +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000894 name: retention time def: "A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000887 ! peptide attribute +is_a: MS:1003050 ! peptidoform attribute +is_a: MS:1003295 ! summary statistics of replicates relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000895 name: local retention time def: "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000896 name: normalized retention time def: "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000894 ! retention time +is_a: MS:1003295 ! summary statistics of replicates relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000897 name: predicted retention time def: "A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000898 @@ -6258,8 +6412,8 @@ is_a: MS:1000901 ! retention time normalization standard id: MS:1000903 name: product ion series ordinal def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001221 ! product ion attribute +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000904 @@ -6272,24 +6426,24 @@ relationship: has_units MS:1000040 ! m/z id: MS:1000905 name: percent of base peak times 100 def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000043 ! intensity unit +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000906 name: peak intensity rank def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000231 ! peak +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000907 name: peak targeting suitability rank def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000231 ! peak +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000908 @@ -6345,19 +6499,19 @@ relationship: part_of MS:1000894 ! retention time id: MS:1000916 name: retention time window lower offset def: "The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000917 name: retention time window upper offset def: "The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000918 @@ -6386,7 +6540,7 @@ is_a: MS:1000919 ! target inclusion exclusion priority [Term] id: MS:1000922 name: Skyline -def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default ""] +def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default] is_a: MS:1000871 ! SRM software is_a: MS:1001139 ! quantitation software name @@ -6414,16 +6568,16 @@ is_a: MS:1000871 ! SRM software id: MS:1000926 name: product interpretation rank def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001221 ! product ion attribute +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000927 name: ion injection time def: "The length of time spent filling an ion trapping device." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000928 @@ -6459,15 +6613,33 @@ is_a: MS:1000121 ! SCIEX instrument model id: MS:1000933 name: protein modifications def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000934 name: gene name def: "Name of the gene from which the protein is translated." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000884 ! protein attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1000935 +name: 6470A Triple Quadrupole LC/MS +def: "The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000936 +name: 6470B Triple Quadrupole LC/MS +def: "The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1000937 +name: 6495C Triple Quadrupole LC/MS +def: "The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1001000 @@ -6478,8 +6650,8 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom [Term] id: MS:1001005 name: SEQUEST:CleavesAt -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001006 @@ -6491,15 +6663,15 @@ is_a: MS:1002096 ! SEQUEST input parameter id: MS:1001007 name: SEQUEST:OutputLines def: "Number of peptide results to show." [PSI:MS] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001009 name: SEQUEST:DescriptionLines def: "Number of full protein descriptions to show for top N peptides." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001010 @@ -6517,8 +6689,8 @@ is_a: MS:1001249 ! search input details id: MS:1001012 name: database source def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001013 @@ -6537,22 +6709,24 @@ is_obsolete: true id: MS:1001015 name: database original uri def: "URI, from where the search database was originally downloaded." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001016 name: database version -def: "OBSOLETE: Use attribute in mzIdentML instead. Version of the search database." [PSI:PI] +def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI] is_a: MS:1001011 ! search database details -is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001017 -name: database release date -def: "OBSOLETE: Use attribute in mzIdentML instead. Release date of the search database." [PSI:PI] +name: release date +def: "Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term." [PSI:PI] is_a: MS:1001011 ! search database details -is_obsolete: true +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:dateTime +relationship: has_structured_representation_in_format MS:1002073 ! mzIdentML format [Term] id: MS:1001018 @@ -6600,14 +6774,14 @@ is_a: MS:1001011 ! search database details id: MS:1001025 name: translation table def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001026 name: SEQUEST:NormalizeXCorrValues -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001027 @@ -6619,23 +6793,23 @@ is_a: MS:1001511 ! Sequence database filter types id: MS:1001028 name: SEQUEST:SequenceHeaderFilter def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001029 name: number of sequences searched def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001030 name: number of peptide seqs compared to each spectrum def: "Number of peptide seqs compared to each spectrum." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001031 @@ -6646,8 +6820,8 @@ is_a: MS:1001080 ! search type [Term] id: MS:1001032 name: SEQUEST:SequencePartialFilter -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001035 @@ -6660,22 +6834,22 @@ is_obsolete: true id: MS:1001036 name: search time taken def: "The time taken to complete the search in seconds." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001184 ! search statistics +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001037 name: SEQUEST:ShowFragmentIons def: "Flag indicating that fragment ions should be shown." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001038 name: SEQUEST:Consensus def: "Specify depth as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001006 ! SEQUEST:ViewCV +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001040 @@ -6693,8 +6867,8 @@ is_a: MS:1001006 ! SEQUEST:ViewCV id: MS:1001042 name: SEQUEST:LimitTo def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002096 ! SEQUEST input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001044 @@ -6712,57 +6886,57 @@ is_a: MS:1001044 ! cleavage agent details id: MS:1001046 name: SEQUEST:sort by dCn def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001047 name: SEQUEST:sort by dM def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001048 name: SEQUEST:sort by Ions def: "Sort order of SEQUEST search results given by the ions." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001049 name: SEQUEST:sort by MH+ def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001050 name: SEQUEST:sort by P def: "Sort order of SEQUEST search results given by the probability." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001051 name: multiple enzyme combination rules def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001052 name: SEQUEST:sort by PreviousAminoAcid def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001053 name: SEQUEST:sort by Ref def: "Sort order of SEQUEST search results given by the reference." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001055 @@ -6793,8 +6967,8 @@ is_a: MS:1001060 ! quality estimation method details id: MS:1001059 name: SEQUEST:sort by RSp def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001060 @@ -6835,36 +7009,36 @@ is_a: MS:1001249 ! search input details id: MS:1001068 name: SEQUEST:sort by Sp def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001069 name: SEQUEST:sort by TIC def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001070 name: SEQUEST:sort by Scan def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001071 name: SEQUEST:sort by Sequence def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001072 name: SEQUEST:sort by Sf def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001073 @@ -6918,8 +7092,8 @@ is_a: MS:1002694 ! single identification result attribute id: MS:1001086 name: SEQUEST:sort by XCorr def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001087 @@ -6931,18 +7105,18 @@ is_a: MS:1002096 ! SEQUEST input parameter id: MS:1001088 name: protein description def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001342 ! database sequence details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001089 name: molecule taxonomy def: "The taxonomy of the resultant molecule from the search." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001342 ! database sequence details is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001090 @@ -6972,56 +7146,56 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute id: MS:1001093 name: sequence coverage def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI] -xref: value-type:xsd\:decimal "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:decimal ! The allowed value-type for this CV term [Term] id: MS:1001094 name: SEQUEST:sort by z def: "Sort order of SEQUEST search results given by the charge." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001041 ! SEQUEST:sortCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001095 name: SEQUEST:ProcessAll -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001096 name: SEQUEST:TopPercentMostIntense def: "Specify \"percentage\" as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001097 name: distinct peptide sequences def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001098 name: confident distinct peptide sequences def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001099 name: confident peptide qualification def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001100 name: confident peptide sequence number def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001101 @@ -7032,14 +7206,14 @@ is_a: MS:1001085 ! protein-level identification attribute [Term] id: MS:1001102 name: SEQUEST:Chromatogram -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001006 ! SEQUEST:ViewCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001103 name: SEQUEST:InfoAndLog -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001006 ! SEQUEST:ViewCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001104 @@ -7057,8 +7231,8 @@ is_a: MS:1002694 ! single identification result attribute id: MS:1001106 name: SEQUEST:TopNumber def: "Specify \"number\" as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001107 @@ -7076,8 +7250,8 @@ is_a: MS:1002473 ! ion series considered in search id: MS:1001109 name: SEQUEST:CullTo def: "Specify cull string as value of the CVParam." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001087 ! SEQUEST:ProcessCV +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001110 @@ -7088,34 +7262,35 @@ is_a: MS:1002096 ! SEQUEST input parameter [Term] id: MS:1001111 name: SEQUEST:Full -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001110 ! SEQUEST:modeCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001112 name: n-terminal flanking residue -def: "The residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001113 name: c-terminal flanking residue -def: "The residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001114 name: retention time(s) def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI] comment: This term was made obsolete because scan start time (MS:1000016) should be used instead. -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute -is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001115 @@ -7133,10 +7308,10 @@ is_a: MS:1001085 ! protein-level identification attribute [Term] id: MS:1001117 name: theoretical mass -def: "The theoretical mass of the molecule (e.g. the peptide sequence and its modifications)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +def: "The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001118 @@ -7153,15 +7328,15 @@ is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001120 name: SEQUEST:FormatAndLinks -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001110 ! SEQUEST:modeCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001121 name: number of matched peaks def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001122 @@ -7173,29 +7348,29 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute id: MS:1001123 name: number of peaks used def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001124 name: number of peaks submitted def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001125 name: manual validation def: "Result of quality estimation: decision of a manual validation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001126 name: SEQUEST:Fast -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001110 ! SEQUEST:modeCV +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001127 @@ -7220,67 +7395,67 @@ id: MS:1001130 name: peptide raw area def: "OBSOLETE Peptide raw area." [PSI:PI] comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001131 name: error on peptide area def: "Error on peptide area." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001132 name: peptide ratio def: "Peptide ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001133 name: error on peptide ratio def: "Error on peptide ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001134 name: protein ratio def: "Protein ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001135 name: error on protein ratio def: "Error on protein ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001136 name: p-value (protein diff from 1 randomly) def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI] comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001137 name: absolute quantity def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001138 name: error on absolute quantity def: "Error on absolute quantity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001139 @@ -7301,8 +7476,8 @@ is_obsolete: true id: MS:1001141 name: intensity of precursor ion def: "The intensity of the precursor ion." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001142 @@ -7379,150 +7554,150 @@ is_a: MS:1002694 ! single identification result attribute id: MS:1001154 name: SEQUEST:probability def: "The SEQUEST result 'Probability'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001155 name: SEQUEST:xcorr def: "The SEQUEST result 'XCorr'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001156 name: SEQUEST:deltacn def: "The SEQUEST result 'DeltaCn'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001157 name: SEQUEST:sp def: "The SEQUEST result 'Sp' (protein)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001158 name: SEQUEST:Uniq -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001159 name: SEQUEST:expectation value def: "The SEQUEST result 'Expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001153 ! search engine specific score +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001160 name: SEQUEST:sf def: "The SEQUEST result 'Sf'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001161 name: SEQUEST:matched ions def: "The SEQUEST result 'Matched Ions'." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001162 name: SEQUEST:total ions def: "The SEQUEST result 'Total Ions'." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001163 name: SEQUEST:consensus score def: "The SEQUEST result 'Consensus Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001153 ! search engine specific score +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001164 name: Paragon:unused protscore def: "The Paragon result 'Unused ProtScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001165 name: Paragon:total protscore def: "The Paragon result 'Total ProtScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001166 name: Paragon:score def: "The Paragon result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001167 name: Paragon:confidence def: "The Paragon result 'Confidence'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001168 name: Paragon:expression error factor def: "The Paragon result 'Expression Error Factor'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001169 name: Paragon:expression change p-value def: "The Paragon result 'Expression change P-value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001170 name: Paragon:contrib def: "The Paragon result 'Contrib'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001171 name: Mascot:score def: "The Mascot result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001172 name: Mascot:expectation value def: "The Mascot result 'expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001173 name: Mascot:matched ions def: "The Mascot result 'Matched ions'." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001174 name: Mascot:total ions def: "The Mascot result 'Total ions'." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001175 @@ -7540,8 +7715,8 @@ is_a: MS:1001180 ! Cleavage agent regular expression id: MS:1001177 name: number of molecular hypothesis considered def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001184 ! search statistics +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001178 @@ -7579,33 +7754,33 @@ id: MS:1001191 name: p-value def: "OBSOLETE Quality estimation by p-value." [PSI:PI] comment: This term was made obsolete because now is split into peptide and protein terms. -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001198 ! protein identification confidence metric is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001192 name: Expect value def: "Result of quality estimation: Expect value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001193 name: confidence score def: "Result of quality estimation: confidence score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001194 name: quality estimation with decoy database def: "Quality estimation by decoy database." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001060 ! quality estimation method details +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001195 @@ -7647,33 +7822,33 @@ is_a: MS:1001040 ! intermediate analysis format id: MS:1001201 name: DB MW filter maximum def: "Maximum value of molecular weight filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001512 ! Sequence database filters relationship: has_units UO:0000221 ! dalton relationship: has_units UO:0000222 ! kilodalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001202 name: DB MW filter minimum def: "Minimum value of molecular weight filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001512 ! Sequence database filters relationship: has_units UO:0000221 ! dalton relationship: has_units UO:0000222 ! kilodalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001203 name: DB PI filter maximum def: "Maximum value of isoelectric point filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001204 name: DB PI filter minimum def: "Minimum value of isoelectric point filter." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001207 @@ -7722,37 +7897,37 @@ is_obsolete: true id: MS:1001214 name: protein-level global FDR def: "Estimation of the global false discovery rate of proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002705 ! protein-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001215 name: SEQUEST:PeptideSp def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001217 name: SEQUEST:PeptideRankSp def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001218 name: SEQUEST:PeptideNumber def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001219 name: SEQUEST:PeptideIdnumber def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI] -xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001220 @@ -7810,6 +7985,7 @@ def: "The product ion m/z error." [PSI:PI] is_a: MS:1001221 ! product ion attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million [Term] id: MS:1001228 @@ -7935,9 +8111,9 @@ relationship: part_of MS:1001000 ! spectrum interpretation id: MS:1001250 name: local FDR def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001251 @@ -8034,22 +8210,22 @@ is_a: MS:1001266 ! role type id: MS:1001268 name: programmer def: "Programmer role." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001266 ! role type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001269 name: instrument vendor def: "Instrument vendor role." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001266 ! role type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001270 name: lab personnel def: "Lab personnel role." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001266 ! role type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001271 @@ -8091,8 +8267,8 @@ is_a: MS:1001040 ! intermediate analysis format id: MS:1001283 name: decoy DB accession regexp def: "Specify the regular expression for decoy accession numbers." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001450 ! decoy DB details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001284 @@ -8212,8 +8388,8 @@ is_obsolete: true id: MS:1001301 name: protein rank def: "The rank of the protein in a list sorted by the search engine." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001085 ! protein-level identification attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001302 @@ -8319,71 +8495,71 @@ relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P) id: MS:1001316 name: Mascot:SigThreshold def: "Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001317 name: Mascot:MaxProteinHits def: "The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001318 name: Mascot:ProteinScoringMethod def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001319 name: Mascot:MinMSMSThreshold def: "Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001320 name: Mascot:ShowHomologousProteinsWithSamePeptides def: "If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001321 name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides def: "If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001322 name: Mascot:RequireBoldRed def: "Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001323 name: Mascot:UseUnigeneClustering def: "If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001324 name: Mascot:IncludeErrorTolerantMatches def: "If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001325 name: Mascot:ShowDecoyMatches def: "If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001326 @@ -8392,33 +8568,40 @@ def: "OBSOLETE." [PSI:PI] comment: This former purgatory term was made obsolete. is_obsolete: true +[Term] +id: MS:1001327 +name: Spectronaut +def: "Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data." [https://doi.org/10.1074/mcp.M114.044305] +is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software + [Term] id: MS:1001328 name: OMSSA:evalue def: "OMSSA E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001329 name: OMSSA:pvalue def: "OMSSA p-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001330 name: X\!Tandem:expect def: "The X!Tandem expectation value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001331 name: X\!Tandem:hyperscore def: "The X!Tandem hyperscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001332 @@ -8580,8 +8763,8 @@ is_a: MS:1001356 ! spectrum descriptions id: MS:1001358 name: msmsEval quality def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001357 ! spectrum quality descriptions +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001359 @@ -8593,23 +8776,23 @@ relationship: part_of MS:1001000 ! spectrum interpretation id: MS:1001360 name: alternate single letter codes def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001359 ! ambiguous residues +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001361 name: alternate mass def: "List of masses a non-standard letter code is replaced with." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001359 ! ambiguous residues relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001362 name: number of unmatched peaks def: "The number of unmatched peaks." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1002345 ! PSM-level attribute +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001363 @@ -8621,9 +8804,9 @@ is_a: MS:1001127 ! peptide sharing details id: MS:1001364 name: peptide sequence-level global FDR def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002703 ! peptide sequence-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001365 @@ -8659,205 +8842,205 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1001370 name: Mascot:homology threshold def: "The Mascot result 'homology threshold'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001371 name: Mascot:identity threshold def: "The Mascot result 'identity threshold'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001372 name: SEQUEST:Sequences -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001373 name: SEQUEST:TIC def: "SEQUEST total ion current." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001374 name: SEQUEST:Sum -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001375 name: Phenyx:Instrument Type def: "The instrument type parameter value in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001376 name: Phenyx:Scoring Model def: "The selected scoring model in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001377 name: Phenyx:Default Parent Charge def: "The default parent charge value in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001378 name: Phenyx:Trust Parent Charge def: "The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001379 name: Phenyx:Turbo def: "The turbo mode parameter in Phenyx." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001380 name: Phenyx:Turbo:ErrorTol def: "The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001381 name: Phenyx:Turbo:Coverage def: "The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001382 name: Phenyx:Turbo:Series def: "The list of ion series considered in the turbo mode of Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001383 name: Phenyx:MinPepLength def: "The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001384 name: Phenyx:MinPepzscore def: "The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001385 name: Phenyx:MaxPepPvalue def: "The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001386 name: Phenyx:AC Score def: "The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001387 name: Phenyx:Conflict Resolution def: "The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002097 ! Phenyx input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001388 name: Phenyx:AC def: "The primary sequence database identifier of a protein in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001389 name: Phenyx:ID -xref: value-type:xsd\:string "The allowed value-type for this CV term." def: "A secondary sequence database identifier of a protein in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001390 name: Phenyx:Score def: "The protein score of a protein match in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001391 name: Phenyx:Peptides1 def: "First number of phenyx result \"#Peptides\"." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001392 name: Phenyx:Peptides2 def: "Second number of phenyx result \"#Peptides\"." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001393 name: Phenyx:Auto def: "The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001394 name: Phenyx:User def: "The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001395 name: Phenyx:Pepzscore def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001396 name: Phenyx:PepPvalue def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001397 name: Phenyx:NumberOfMC def: "The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001398 name: Phenyx:Modif def: "The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001399 @@ -8911,8 +9094,8 @@ is_a: MS:1002473 ! ion series considered in search id: MS:1001410 name: translation start codons def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001411 @@ -8923,77 +9106,77 @@ is_a: MS:1001249 ! search input details [Term] id: MS:1001412 name: search tolerance plus value -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001411 ! search tolerance specification relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001413 name: search tolerance minus value -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001411 ! search tolerance specification relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001414 name: MGF scans def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000797 +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001415 name: MGF raw scans def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000798 +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001416 name: spectrum title def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000796 +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001417 name: SpectraST:dot def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001418 name: SpectraST:dot_bias def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001419 name: SpectraST:discriminant score F def: "SpectraST spectrum score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001420 name: SpectraST:delta def: "SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001421 @@ -9011,189 +9194,189 @@ is_a: MS:1001040 ! intermediate analysis format id: MS:1001423 name: translation table description def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001424 name: ProteinExtractor:Methodname def: "Name of the used method in the ProteinExtractor algorithm." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001425 name: ProteinExtractor:GenerateNonRedundant def: "Flag indicating if a non redundant scoring should be generated." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001426 name: ProteinExtractor:IncludeIdentified def: "Flag indicating if identified proteins should be included." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001427 name: ProteinExtractor:MaxNumberOfProteins def: "The maximum number of proteins to consider." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001428 name: ProteinExtractor:MaxProteinMass def: "The maximum considered mass for a protein." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001429 name: ProteinExtractor:MinNumberOfPeptides def: "The minimum number of proteins to consider." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001430 name: ProteinExtractor:UseMascot def: "Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001431 name: ProteinExtractor:MascotPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001432 name: ProteinExtractor:MascotUniqueScore def: "In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001433 name: ProteinExtractor:MascotUseIdentityScore -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001434 name: ProteinExtractor:MascotWeighting def: "Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001435 name: ProteinExtractor:UseSequest def: "Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001436 name: ProteinExtractor:SequestPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001437 name: ProteinExtractor:SequestUniqueScore def: "In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001438 name: ProteinExtractor:SequestWeighting def: "Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001439 name: ProteinExtractor:UseProteinSolver def: "Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001440 name: ProteinExtractor:ProteinSolverPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001441 name: ProteinExtractor:ProteinSolverUniqueScore def: "In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001442 name: ProteinExtractor:ProteinSolverWeighting def: "Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001443 name: ProteinExtractor:UsePhenyx def: "Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001444 name: ProteinExtractor:PhenyxPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001445 name: ProteinExtractor:PhenyxUniqueScore def: "In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001446 name: ProteinExtractor:PhenyxWeighting def: "Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001447 name: prot:FDR threshold def: "False-discovery rate threshold for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002485 ! protein-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001448 name: pep:FDR threshold def: "False-discovery rate threshold for peptides." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002484 ! peptide-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001449 name: OMSSA e-value threshold def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002099 ! OMSSA input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001450 @@ -9205,8 +9388,8 @@ is_a: MS:1001011 ! search database details id: MS:1001451 name: decoy DB generation algorithm def: "Name of algorithm used for decoy generation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001450 ! decoy DB details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001452 @@ -9297,29 +9480,29 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1001467 name: taxonomy: NCBI TaxID def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001468 name: taxonomy: common name def: "This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001469 name: taxonomy: scientific name def: "This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001470 name: taxonomy: Swiss-Prot ID def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001089 ! molecule taxonomy +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001471 @@ -9330,27 +9513,24 @@ relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001472 name: selected ion monitoring chromatogram -def: "Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point." [PSI:MS] +def: "Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS] synonym: "SIM chromatogram" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000810 ! mass chromatogram +is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1001473 name: selected reaction monitoring chromatogram -def: "Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point." [PSI:MS] +def: "Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS] synonym: "SRM chromatogram" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000810 ! mass chromatogram +is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1001474 name: consecutive reaction monitoring chromatogram -def: "OBSOLETE Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point." [PSI:MS] +def: "OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS] comment: This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way. synonym: "CRM chromatogram" EXACT [] -is_a: MS:1000524 ! data file content -is_a: MS:1000810 ! mass chromatogram +is_a: MS:1000810 ! ion current chromatogram is_obsolete: true [Term] @@ -9368,8 +9548,10 @@ is_a: MS:1001456 ! analysis software [Term] id: MS:1001477 name: SpectraST -def: "SpectraST was used to analyze the spectra." [PSI:PI] +def: "Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline." [PSI:PI] is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software +is_a: MS:1003406 ! spectrum clustering software [Term] id: MS:1001478 @@ -9458,22 +9640,22 @@ is_a: MS:1001456 ! analysis software id: MS:1001491 name: percolator:Q value def: "Percolator:Q value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001492 name: percolator:score def: "Percolator:score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001493 name: percolator:PEP def: "Posterior error probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001494 @@ -9485,92 +9667,92 @@ is_a: MS:1002482 ! statistical threshold id: MS:1001495 name: ProteinScape:SearchResultId def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001496 name: ProteinScape:SearchEventId def: "The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001497 name: ProteinScape:ProfoundProbability def: "The Profound probability score stored by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001498 name: Profound:z value def: "The Profound z value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001499 name: Profound:Cluster def: "The Profound cluster score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001500 name: Profound:ClusterRank def: "The Profound cluster rank." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001501 name: MSFit:Mowse score def: "The MSFit Mowse score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001502 name: Sonar:Score def: "The Sonar score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001503 name: ProteinScape:PFFSolverExp def: "The ProteinSolver exp value stored by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001504 name: ProteinScape:PFFSolverScore def: "The ProteinSolver score stored by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001505 name: ProteinScape:IntensityCoverage def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001506 name: ProteinScape:SequestMetaScore def: "The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001507 name: ProteinExtractor:Score def: "The score calculated by ProteinExtractor." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001508 @@ -9606,15 +9788,15 @@ is_a: MS:1001019 ! database filtering id: MS:1001513 name: DB sequence filter pattern def: "DB sequence filter pattern." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001514 name: DB accession filter string def: "DB accession filter string." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001512 ! Sequence database filters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001515 @@ -9674,17 +9856,17 @@ is_a: MS:1002307 ! fragmentation ion type id: MS:1001524 name: fragment neutral loss def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001525 name: precursor neutral loss def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001526 @@ -9941,43 +10123,43 @@ is_a: MS:1001040 ! intermediate analysis format id: MS:1001568 name: Scaffold:Peptide Probability def: "Scaffold peptide probability score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001569 name: IdentityE Score def: "Waters IdentityE peptide score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001570 name: ProteinLynx:Log Likelihood def: "ProteinLynx log likelihood score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001571 name: ProteinLynx:Ladder Score def: "Waters ProteinLynx Ladder score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001572 name: SpectrumMill:Score def: "Spectrum mill peptide score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001573 name: SpectrumMill:SPI def: "SpectrumMill SPI score (%)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001574 @@ -9989,50 +10171,54 @@ is_a: MS:1001060 ! quality estimation method details id: MS:1001575 name: Scaffold: Minimum Peptide Count def: "Minimum number of peptides a protein must have to be accepted." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002106 ! Scaffold input parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001576 name: Scaffold: Minimum Protein Probability def: "Minimum protein probability a protein must have to be accepted." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002106 ! Scaffold input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001577 name: Scaffold: Minimum Peptide Probability def: "Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002106 ! Scaffold input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001578 name: minimum number of enzymatic termini def: "Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1002094 ! common search engine input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001579 name: Scaffold:Protein Probability def: "Scaffold protein probability score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001580 name: SpectrumMill:Discriminant Score def: "Discriminant score from Agilent SpectrumMill software." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001581 name: FAIMS compensation voltage def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS CV" EXACT [] -is_a: MS:1000503 ! scan attribute +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001582 @@ -10098,15 +10284,15 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic id: MS:1001591 name: anchor protein def: "A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001592 name: family member protein def: "A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001593 @@ -10118,1099 +10304,1099 @@ is_a: MS:1001101 ! protein group or subset relationship id: MS:1001594 name: sequence same-set protein def: "A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001595 name: spectrum same-set protein def: "A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001596 name: sequence sub-set protein def: "A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001597 name: spectrum sub-set protein def: "A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001598 name: sequence subsumable protein def: "A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001599 name: spectrum subsumable protein def: "A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001600 name: protein inference confidence category def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001601 name: ProteomeDiscoverer:Spectrum Files:Raw File names def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001602 name: ProteomeDiscoverer:SRF File Selector:SRF File Path def: "OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS] comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001603 name: ProteomeDiscoverer:Spectrum Selector:Ionization Source def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001604 name: ProteomeDiscoverer:Activation Type def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001605 name: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit def: "Lower retention-time limit." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001606 name: ProteomeDiscoverer:Mass Analyzer def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS)." [PSI:MS] comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001607 name: ProteomeDiscoverer:Max Precursor Mass def: "Maximum mass limit of a singly charged precursor ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001608 name: ProteomeDiscoverer:Min Precursor Mass def: "Minimum mass limit of a singly charged precursor ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001609 name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count def: "Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001610 name: ProteomeDiscoverer:MS Order def: "OBSOLETE Level of the mass spectrum (MS2 ... MS10)." [PSI:MS] comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001611 name: ProteomeDiscoverer:Polarity Mode def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001612 name: ProteomeDiscoverer:Spectrum Selector:Precursor Selection def: "Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001613 name: ProteomeDiscoverer:SN Threshold def: "Signal-to-Noise ratio below which peaks are removed." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001614 name: ProteomeDiscoverer:Scan Type def: "OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS] comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001615 name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold def: "Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001616 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements def: "Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001617 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements def: "Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001618 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements def: "Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001619 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements def: "Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001620 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements def: "Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001621 name: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit def: "Upper retention-time limit." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001622 name: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset def: "Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001623 name: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass def: "Maximum allowed mass of a neutral loss." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001624 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor def: "Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001625 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks def: "Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001626 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses def: "Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001627 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones def: "Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001628 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak def: "Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001629 name: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch def: "Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001630 name: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch def: "Determines whether spectra from different MS order scans can be grouped together." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001631 name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference def: "OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species." [PSI:MS] comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001632 name: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion def: "Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001633 name: ProteomeDiscoverer:Xtract:Highest Charge def: "Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001634 name: ProteomeDiscoverer:Xtract:Highest MZ def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001635 name: ProteomeDiscoverer:Xtract:Lowest Charge def: "Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001636 name: ProteomeDiscoverer:Xtract:Lowest MZ def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001637 name: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only def: "Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001638 name: ProteomeDiscoverer:Xtract:Overlapping Remainder def: "Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001639 name: ProteomeDiscoverer:Xtract:Required Fitting Accuracy def: "Accuracy required for a pattern fit to be considered valid." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001640 name: ProteomeDiscoverer:Xtract:Resolution At 400 def: "Resolution at mass 400." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001641 name: ProteomeDiscoverer:Lowest Charge State def: "Minimum charge state below which peptides are filtered out." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001642 name: ProteomeDiscoverer:Highest Charge State def: "Maximum charge above which peptides are filtered out." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001643 name: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores def: "Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001644 name: ProteomeDiscoverer:Dynamic Modification def: "Determine dynamic post-translational modifications (PTMs)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001645 name: ProteomeDiscoverer:Static Modification def: "Static Modification to all occurrences of a named amino acid." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001646 name: ProteomeDiscoverer:Mascot:Decoy Search def: "OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database." [PSI:MS] comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001647 name: ProteomeDiscoverer:Mascot:Error tolerant Search def: "Determines whether to search error-tolerant." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001648 name: ProteomeDiscoverer:Mascot:Max MGF File Size def: "Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001649 name: ProteomeDiscoverer:Mascot:Mascot Server URL def: "URL (Uniform resource Locator) of the Mascot server." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001650 name: ProteomeDiscoverer:Mascot:Number of attempts to submit the search def: "Number of attempts to submit the Mascot search." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001651 name: ProteomeDiscoverer:Mascot:X Static Modification def: "Number of attempts to submit the Mascot search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001652 name: ProteomeDiscoverer:Mascot:User Name def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS] comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001653 name: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search def: "Time interval between attempts to submit a search in seconds." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001654 name: ProteomeDiscoverer:Enzyme Name def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS] comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001655 name: ProteomeDiscoverer:Fragment Mass Tolerance def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [PSI:MS] comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001656 name: Mascot:Instrument def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001657 name: ProteomeDiscoverer:Maximum Missed Cleavage Sites def: "Maximum number of missed cleavage sites to consider during the digest." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001658 name: ProteomeDiscoverer:Mascot:Peptide CutOff Score def: "Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001659 name: ProteomeDiscoverer:Precursor Mass Tolerance def: "OBSOLETE Mass window for which precursor ions are considered to be the same species." [PSI:MS] comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001660 name: ProteomeDiscoverer:Mascot:Protein CutOff Score def: "Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001661 name: ProteomeDiscoverer:Protein Database def: "OBSOLETE Database to use in the search (configured on the Mascot server)." [PSI:MS] comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001662 name: ProteomeDiscoverer:Mascot:Protein Relevance Factor def: "Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001663 name: ProteomeDiscoverer:Target FDR Relaxed def: "Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001664 name: ProteomeDiscoverer:Target FDR Strict def: "Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001665 name: ProteomeDiscoverer:Mascot:Taxonomy def: "OBSOLETE Limits searches to entries from a particular species or group of species." [PSI:MS] comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001666 name: ProteomeDiscoverer:Use Average Precursor Mass def: "OBSOLETE Use average mass for the precursor." [PSI:MS] comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001667 name: Mascot:use MudPIT scoring def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS] comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001668 name: ProteomeDiscoverer:Absolute XCorr Threshold def: "Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001669 name: ProteomeDiscoverer:SEQUEST:Calculate Probability Score def: "Determines whether to calculate a probability score for every peptide match." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001670 name: ProteomeDiscoverer:SEQUEST:CTerminal Modification def: "Dynamic C-terminal modification that is used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001671 name: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage def: "Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001672 name: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide def: "Maximum number of identical modifications that a single peptide can have." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001673 name: ProteomeDiscoverer:Max Modifications Per Peptide def: "Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001674 name: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered def: "Maximum number of peptides that are searched and scored per spectrum." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001675 name: ProteomeDiscoverer:Maximum Peptides Output def: "Maximum number of peptide matches reported per spectrum." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001676 name: ProteomeDiscoverer:Maximum Protein References Per Peptide def: "Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001677 name: ProteomeDiscoverer:SEQUEST:NTerminal Modification def: "Dynamic N-terminal modification that is used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001678 name: ProteomeDiscoverer:Peptide CTerminus def: "Static modification for the C terminal of the peptide used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001679 name: ProteomeDiscoverer:Peptide NTerminus def: "Static modification for the N terminal of the peptide used during the search." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001680 name: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor def: "Specifies a factor to apply to the protein score." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001681 name: ProteomeDiscoverer:Protein Relevance Threshold def: "Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001682 name: ProteomeDiscoverer:Search Against Decoy Database def: "OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database." [PSI:MS] comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001683 name: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses def: "Use average masses for the fragments." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001684 name: ProteomeDiscoverer:Use Neutral Loss a Ions def: "Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001685 name: ProteomeDiscoverer:Use Neutral Loss b Ions def: "Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001686 name: ProteomeDiscoverer:Use Neutral Loss y Ions def: "Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001687 name: ProteomeDiscoverer:Use Neutral Loss z Ions def: "Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001688 name: ProteomeDiscoverer:SEQUEST:Weight of a Ions def: "Uses a ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001689 name: ProteomeDiscoverer:SEQUEST:Weight of b Ions def: "Uses b ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001690 name: ProteomeDiscoverer:SEQUEST:Weight of c Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001691 name: ProteomeDiscoverer:SEQUEST:Weight of d Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001692 name: ProteomeDiscoverer:SEQUEST:Weight of v Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001693 name: ProteomeDiscoverer:SEQUEST:Weight of w Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001694 name: ProteomeDiscoverer:SEQUEST:Weight of x Ions def: "Uses x ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001695 name: ProteomeDiscoverer:SEQUEST:Weight of y Ions def: "Uses y ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001696 name: ProteomeDiscoverer:SEQUEST:Weight of z Ions def: "Uses z ions for spectrum matching with this relative factor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001697 name: ProteomeDiscoverer:ZCore:Protein Score Cutoff def: "Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001698 name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method def: "Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001699 name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance def: "Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001700 name: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method def: "Quantitation method for isobarically labeled quantitation." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001701 name: ProteomeDiscoverer:Spectrum Exporter:Export Format def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001702 name: ProteomeDiscoverer:Spectrum Exporter:File name def: "Name of the output file that contains the exported data." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001703 name: ProteomeDiscoverer:Search Modifications Only For Identified Proteins def: "Influences the modifications search." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001704 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 def: "Standard high confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001705 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 def: "Standard high confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001706 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 def: "Standard high confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001707 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 def: "Standard high confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001708 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 def: "Standard medium confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001709 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 def: "Standard medium confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001710 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 def: "Standard medium confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001711 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 def: "Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001712 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 def: "FT high confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001713 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 def: "FT high confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001714 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 def: "FT high confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001715 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 def: "FT high confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001716 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 def: "FT medium confidence XCorr parameter for charge = 1." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001717 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 def: "FT medium confidence XCorr parameter for charge = 2." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001718 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 def: "FT medium confidence XCorr parameter for charge = 3." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001719 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 def: "FT medium confidence XCorr parameter for charge >= 4." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001720 name: ProteomeDiscoverer:1. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001721 name: ProteomeDiscoverer:2. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001722 name: ProteomeDiscoverer:3. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001723 name: ProteomeDiscoverer:4. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001724 name: ProteomeDiscoverer:Static Modification for X def: "Static Modification for X." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001725 name: ProteomeDiscoverer:Initial minimal peptide probability def: "Minimal initial peptide probability to contribute to analysis." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001726 name: ProteomeDiscoverer:Minimal peptide probability def: "Minimum adjusted peptide probability contributing to protein probability." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001727 name: ProteomeDiscoverer:Minimal peptide weight def: "Minimum peptide weight contributing to protein probability." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001728 name: ProteomeDiscoverer:Number of input1 spectra def: "Number of spectra from 1+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001729 name: ProteomeDiscoverer:Number of input2 spectra def: "Number of spectra from 2+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001730 name: ProteomeDiscoverer:Number of input3 spectra def: "Number of spectra from 3+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001731 name: ProteomeDiscoverer:Number of input4 spectra def: "Number of spectra from 4+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001732 name: ProteomeDiscoverer:Number of input5 spectra def: "Number of spectra from 5+ precursor ions." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001733 name: ProteomeDiscoverer:Number of predicted correct proteins def: "Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001734 name: ProteomeDiscoverer:Organism def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS] comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001735 name: ProteomeDiscoverer:Reference Database def: "OBSOLETE Full path database name." [PSI:MS] comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001736 name: ProteomeDiscoverer:Residue substitution list def: "Residues considered equivalent when comparing peptides." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001737 name: ProteomeDiscoverer:Source file extension def: "OBSOLETE File type (if not pepXML)." [PSI:MS] comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001738 name: ProteomeDiscoverer:Source Files def: "OBSOLETE Input pepXML files." [PSI:MS] comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001739 name: ProteomeDiscoverer:Source Files old def: "OBSOLETE Input pepXML files (old)." [PSI:MS] comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001740 name: ProteomeDiscoverer:WinCyg reference database def: "Windows full path for database." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001741 name: ProteomeDiscoverer:WinCyg source files def: "Windows pepXML file names." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001742 @@ -11222,127 +11408,127 @@ is_a: MS:1000494 ! Thermo Scientific instrument model id: MS:1001743 name: ProteomeDiscoverer:Mascot:Weight of A Ions def: "Determines if to use A ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001744 name: ProteomeDiscoverer:Mascot:Weight of B Ions def: "Determines if to use B ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001745 name: ProteomeDiscoverer:Mascot:Weight of C Ions def: "Determines if to use C ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001746 name: ProteomeDiscoverer:Mascot:Weight of D Ions def: "Determines if to use D ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001747 name: ProteomeDiscoverer:Mascot:Weight of V Ions def: "Determines if to use V ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001748 name: ProteomeDiscoverer:Mascot:Weight of W Ions def: "Determines if to use W ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001749 name: ProteomeDiscoverer:Mascot:Weight of X Ions def: "Determines if to use X ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001750 name: ProteomeDiscoverer:Mascot:Weight of Y Ions def: "Determines if to use Y ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001751 name: ProteomeDiscoverer:Mascot:Weight of Z Ions def: "Determines if to use z ions for spectrum matching." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001752 name: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation def: "Determines if to use precursor reevaluation." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001753 name: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly def: "Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001754 name: ProteomeDiscoverer:Mascot:Please Do not Touch this def: "Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001755 name: contact phone number def: "Phone number of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001756 name: contact fax number def: "Fax number for the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001757 name: contact toll-free phone number def: "Toll-free phone number of the contact person or organization." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000585 ! contact attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001758 name: Mascot:SigThresholdType def: "Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001759 name: Mascot:ProteinGrouping def: "Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering')." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001760 name: Percolator:features def: "List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002107 ! Percolator input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001761 @@ -11540,8 +11726,8 @@ is_a: MS:1000126 ! Waters instrument model id: MS:1001793 name: Mascot:PreferredTaxonomy def: "NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001795 @@ -11634,8 +11820,8 @@ is_a: MS:1001806 ! quantification object attribute id: MS:1001808 name: technical replicate def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001809 @@ -11671,22 +11857,22 @@ is_a: MS:1001807 ! study variable attribute id: MS:1001814 name: generic experimental condition def: "The experimental condition is given in the value of this term." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001815 name: time series, time point X def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001816 name: dilution series, concentration X def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001807 ! study variable attribute +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001817 @@ -11764,8 +11950,8 @@ is_a: MS:1001806 ! quantification object attribute id: MS:1001829 name: SRM transition ID def: "Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001828 ! feature attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001830 @@ -11784,8 +11970,8 @@ is_a: MS:1000752 ! TOPP software id: MS:1001832 name: quantitation software comment or customizations def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001129 ! quantification information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001833 @@ -11815,7 +12001,6 @@ is_a: MS:1001833 ! quantitation analysis summary id: MS:1001837 name: iTRAQ quantitation analysis def: "Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range." [PSI:PI, PMID:15385600] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] @@ -11834,59 +12019,59 @@ is_a: MS:1001833 ! quantitation analysis summary id: MS:1001840 name: LC-MS feature intensity def: "Maximum peak intensity of the LC-MS feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001841 name: LC-MS feature volume def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001843 name: MS1 feature maximum intensity def: "Maximum intensity of MS1 feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001844 name: MS1 feature area def: "Area of MS1 feature." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001845 name: peak area def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] comment: This term was made obsolete because it was a duplication of MS:1001844. -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001846 name: isotopic pattern area def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001847 name: reporter ion intensity def: "Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001848 @@ -11899,86 +12084,86 @@ id: MS:1001849 name: sum of MatchedFeature values def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI] comment: This term was made obsolete because the concept MatchedFeature was dropped. -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001850 name: normalized peptide value def: "Normalized peptide value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001851 name: protein value: sum of peptide values def: "Protein quantification value calculated as sum of peptide values." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001852 name: normalized protein value def: "Normalized protein value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001853 name: max fold change def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001854 name: ANOVA p-value def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002072 ! p-value +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001855 name: t-test p-value def: "P-value of t-Test of two groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002072 ! p-value +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001856 name: reporter ion raw value def: "Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001857 name: reporter ion normalized value def: "Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001858 name: XIC area def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001859 name: normalized XIC area def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001860 name: protein value: mean of peptide ratios def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001861 @@ -12026,66 +12211,66 @@ is_a: MS:1001861 ! quantification data processing id: MS:1001868 name: distinct peptide-level q-value def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002484 ! peptide-level statistical threshold relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001869 name: protein-level q-value def: "Estimation of the q-value for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001870 name: peptide sequence-level p-value def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001871 name: protein-level p-value def: "Estimation of the p-value for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001872 name: peptide sequence-level e-value def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001873 name: protein-level e-value def: "Estimation of the e-value for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001874 name: FDRScore def: "OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293] comment: This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374). -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001875 name: modification motif def: "The regular expression describing the sequence motif for a modification." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001056 ! modification specificity rule +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001876 @@ -12106,18 +12291,15 @@ is_a: MS:1001798 ! LECO software id: MS:1001878 name: MALDI Solutions Microbial Identification def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] -is_a: MS:1001455 ! acquisition software -is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software is_a: MS:1001558 ! MALDI Solutions [Term] id: MS:1001879 name: offset voltage def: "The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001880 @@ -12141,22 +12323,23 @@ relationship: part_of MS:1000908 ! transition id: MS:1001883 name: coefficient of variation def: "Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001882 ! transition validation attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001884 name: signal-to-noise ratio def: "Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001882 ! transition validation attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001885 name: command-line parameters def: "Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001886 @@ -12187,129 +12370,129 @@ is_a: MS:1002363 ! search engine specific score for proteins id: MS:1001890 name: Progenesis:protein normalised abundance def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001891 name: Progenesis:peptide normalised abundance def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001892 name: Progenesis:protein raw abundance def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001893 name: Progenesis:peptide raw abundance def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001894 name: Progenesis:confidence score def: "The data type confidence score produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001895 name: Progenesis:peptide count def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001896 name: Progenesis:feature intensity def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001897 name: MaxQuant:peptide counts (unique) def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001898 name: MaxQuant:peptide counts (all) def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001899 name: MaxQuant:peptide counts (razor+unique) def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001900 name: MaxQuant:sequence length def: "The data type sequence length produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001901 name: MaxQuant:PEP def: "The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001902 name: MaxQuant:LFQ intensity def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001903 name: MaxQuant:feature intensity def: "The data type feature intensity produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001904 name: MaxQuant:MS/MS count def: "The data type MS2 count produced by MaxQuant." [PSI:MS] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001905 name: emPAI value def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001906 name: APEX value def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001907 name: retention time window width def: "The full width of a retention time window for a chromatographic peak." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001908 @@ -12326,7 +12509,7 @@ is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001910 name: LTQ Orbitrap Elite -def: "Thermo Scientific second generation Velos and Orbitrap." [PSI:MS] +def: "Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] @@ -12347,9 +12530,9 @@ is_a: MS:1001457 ! data processing software id: MS:1001913 name: S-lens voltage def: "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001914 @@ -12391,80 +12574,80 @@ relationship: has_regexp MS:1001960 ! (?<=W) id: MS:1001919 name: ProteomeXchange accession number def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001921 name: ProteomeXchange accession number version number def: "Version number of a ProteomeXchange accession number." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001922 name: Digital Object Identifier (DOI) def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org] -xref: value-type:xsd\:string "The allowed value-type for this CV term." synonym: "doi" EXACT [] is_a: MS:1000878 ! external reference identifier relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+) +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1000878 ! external reference identifier +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001924 name: journal article keyword def: "Keyword present in a scientific publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001925 name: submitter keyword def: "Keyword assigned by the data submitter." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001926 name: curator keyword def: "Keyword assigned by a data curator." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001923 ! external reference keyword +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001927 name: Tranche file hash def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001928 name: Tranche project hash def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001929 name: PRIDE experiment URI def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001930 name: PRIDE project URI def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001931 @@ -12476,15 +12659,15 @@ relationship: part_of MS:1000458 ! source id: MS:1001932 name: source interface model def: "The source interface model." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001931 ! source interface +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001933 name: source sprayer def: "The source sprayer." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1000458 ! source +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001934 @@ -12496,15 +12679,15 @@ relationship: part_of MS:1001933 ! source sprayer id: MS:1001935 name: source sprayer manufacturer def: "The source sprayer manufacturer." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001936 name: source sprayer model def: "The source sprayer model." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001933 ! source sprayer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001937 @@ -12552,10 +12735,10 @@ is_a: MS:1001941 ! electrospray supply type id: MS:1001944 name: Collision cell exit potential def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000218 ! volt synonym: "CXP" EXACT [] +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001945 @@ -12597,36 +12780,36 @@ is_a: MS:1000531 ! software id: MS:1001950 name: PEAKS:peptideScore def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001951 name: PEAKS:proteinScore def: "The PEAKS protein '-10lgP Score'." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001952 name: ZCore:probScore def: "The ZCore probability score." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001953 name: source interface manufacturer def: "The source interface manufacturer." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001931 ! source interface +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001954 name: acquisition parameter def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001458 ! spectrum generation information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001955 @@ -12668,36 +12851,36 @@ is_a: MS:1001180 ! Cleavage agent regular expression id: MS:1001961 name: peptide spectrum match scoring algorithm def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:1001458 ! spectrum generation information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001962 name: Mascot:C13 counts def: "C13 peaks to use in peak detection." [PSI:MS] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001963 name: ProteinExtractor:Weighting def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002098 ! ProteinExtractor input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001964 name: ProteinScape:second round Mascot def: "Flag indicating a second round search with Mascot." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002100 ! ProteinScape input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001965 name: ProteinScape:second round Phenyx def: "Flag indicating a second round search with Phenyx." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002100 ! ProteinScape input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001966 @@ -12709,11 +12892,11 @@ is_a: MS:1001221 ! product ion attribute id: MS:1001967 name: product ion drift time def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002222 ! SRM transition attribute relationship: has_units UO:0000028 ! millisecond comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). is_obsolete: true +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001968 @@ -12725,32 +12908,32 @@ is_a: MS:1002689 ! PTM localization single result statistic id: MS:1001969 name: phosphoRS score def: "phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001970 name: phosphoRS sequence probability def: "Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001971 name: phosphoRS site probability def: "Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001972 name: PTM scoring algorithm version def: "Version of the post-translational modification scoring algorithm." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001973 @@ -12762,32 +12945,34 @@ is_a: MS:1001456 ! analysis software id: MS:1001974 name: DeBunker:score def: "Score specific to DeBunker." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001975 name: delta m/z def: "The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value." [PSI:MS] synonym: "m/z difference" EXACT [] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001976 name: delta M def: "The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value." [PSI:MS] synonym: "mass difference" EXACT [] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000166 ! parts per notation unit +relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001977 @@ -12799,48 +12984,48 @@ is_a: MS:1001456 ! analysis software id: MS:1001978 name: MSQuant:PTM-score def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001979 name: MaxQuant:PTM Score def: "The PTM score from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001980 name: MaxQuant:Phospho (STY) Probabilities def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001981 name: MaxQuant:Phospho (STY) Score Diffs def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001982 name: MaxQuant:P-site localization probability def: "The P-site localization probability value from MaxQuant software." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001983 name: MaxQuant:PTM Delta Score def: "The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001984 @@ -12852,17 +13037,17 @@ is_a: MS:1001456 ! analysis software id: MS:1001985 name: Ascore def: "A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001986 name: H-Score def: "H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001987 @@ -12953,29 +13138,29 @@ is_a: MS:1000044 ! dissociation method id: MS:1002001 name: MS1 label-based raw feature quantitation def: "MS1 label-based raw feature quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002002 name: MS1 label-based peptide level quantitation def: "MS1 label-based peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002003 name: MS1 label-based protein level quantitation def: "MS1 label-based protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002004 name: MS1 label-based proteingroup level quantitation def: "MS1 label-based proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002005 @@ -13014,7 +13199,6 @@ is_a: MS:1001833 ! quantitation analysis summary id: MS:1002010 name: TMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] @@ -13028,46 +13212,46 @@ is_a: MS:1000240 ! atmospheric pressure ionization id: MS:1002012 name: Mascot:PTM site assignment confidence def: "Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002013 name: collision energy ramp start def: "Collision energy at the start of the collision energy ramp." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000045 ! collision energy relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002014 name: collision energy ramp end def: "Collision energy at the end of the collision energy ramp." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000045 ! collision energy relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002015 name: spectral count peptide level quantitation def: "Spectral count peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001836 ! spectral counting quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002016 name: spectral count protein level quantitation def: "Spectral count protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001836 ! spectral counting quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002017 name: spectral count proteingroup level quantitation def: "Spectral count proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001836 ! spectral counting quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002018 @@ -13079,29 +13263,29 @@ is_a: MS:1001833 ! quantitation analysis summary id: MS:1002019 name: label-free raw feature quantitation def: "Label-free raw feature quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002020 name: label-free peptide level quantitation def: "Label-free peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002021 name: label-free protein level quantitation def: "Label-free protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002022 name: label-free proteingroup level quantitation def: "Label-free proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002023 @@ -13113,64 +13297,64 @@ is_a: MS:1001833 ! quantitation analysis summary id: MS:1002024 name: MS2 tag-based feature level quantitation def: "MS2 tag-based feature level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002025 name: MS2 tag-based peptide level quantitation def: "MS2 tag-based peptide level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002026 name: MS2 tag-based protein level quantitation def: "MS2 tag-based protein level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002027 name: MS2 tag-based proteingroup level quantitation def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002028 name: nucleic acid base modification def: "Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002029 name: original nucleic acid sequence def: "Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002030 name: modified nucleic acid sequence def: "Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002031 name: PASSEL transition group browser URI def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002032 name: PeptideAtlas dataset URI def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002033 @@ -13204,9 +13388,9 @@ is_a: MS:1002033 ! contact role [Term] id: MS:1002038 -name: unlabeled sample +name: label free sample def: "A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI] -synonym: "light labeled sample" EXACT [] +synonym: "light sample" EXACT [] is_a: MS:1000548 ! sample attribute [Term] @@ -13220,29 +13404,29 @@ relationship: part_of MS:1000458 ! source id: MS:1002040 name: inlet temperature def: "The temperature of the inlet of a mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute is_a: MS:1002039 ! inlet attribute relationship: has_units UO:0000012 ! kelvin relationship: has_units UO:0000027 ! degree Celsius +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002041 name: source temperature def: "The temperature of the source of a mass spectrometer." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000482 ! source attribute relationship: has_units UO:0000012 ! kelvin relationship: has_units UO:0000027 ! degree Celsius +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002042 name: modulation time def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column." [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000857 ! run attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002043 @@ -13254,22 +13438,22 @@ is_a: MS:1001456 ! analysis software id: MS:1002044 name: ProteinProspector:score def: "The ProteinProspector result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002045 name: ProteinProspector:expectation value def: "The ProteinProspector result 'Expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002046 name: native source path def: "The original source path used for directory-based sources." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001458 ! spectrum generation information +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002047 @@ -13288,62 +13472,62 @@ is_a: MS:1001456 ! analysis software id: MS:1002049 name: MS-GF:RawScore def: "MS-GF raw score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002050 name: MS-GF:DeNovoScore def: "MS-GF de novo score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002051 name: MS-GF:Energy def: "MS-GF energy score." [PSI:PI] -xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002052 name: MS-GF:SpecEValue def: "MS-GF spectral E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002053 name: MS-GF:EValue def: "MS-GF E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002054 name: MS-GF:QValue def: "MS-GF Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002055 name: MS-GF:PepQValue def: "MS-GF peptide-level Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002056 name: MS-GF:PEP def: "MS-GF posterior error probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002057 @@ -13392,29 +13576,29 @@ is_a: MS:1001139 ! quantitation software name id: MS:1002064 name: peptide consensus RT def: "Peptide consensus retention time." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002065 name: peptide consensus m/z def: "Peptide consensus mass/charge ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002066 name: ratio calculation method def: "Method used to calculate the ratio." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002067 name: protein value: median of peptide ratios def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002068 @@ -13426,30 +13610,30 @@ is_a: MS:1001055 ! modification parameters id: MS:1002069 name: metabolic labelling purity def: "Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001055 ! modification parameters +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002070 name: t-test def: "Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001861 ! quantification data processing +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002071 name: ANOVA-test def: "Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001861 ! quantification data processing +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002072 name: p-value def: "P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002073 @@ -13486,52 +13670,52 @@ id: MS:1002078 name: ProteomeDiscoverer:1. Static Modification def: "OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002079 name: ProteomeDiscoverer:2. Static Modification def: "OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002080 name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before def: "Precursor clipping range before." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002081 name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After def: "Precursor clipping range after." [PSI:MS] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002082 name: first column elution time def: "The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002083 name: second column elution time def: "The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002084 @@ -13567,29 +13751,29 @@ is_a: MS:1002084 ! multidimensional chromatography modulation description id: MS:1002089 name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold def: "XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002090 name: Calculate Probability Scores def: "Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002094 ! common search engine input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002091 name: ProteomeDiscoverer:Maximum Delta Cn def: "Delta Cn threshold for filtering out PSM's." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002092 name: Percolator:Validation based on def: "Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002107 ! Percolator input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002093 @@ -13782,10 +13966,10 @@ id: MS:1002125 name: combined FDRScore def: "OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] comment: This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375). -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score is_obsolete: true +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002126 @@ -13954,8 +14138,8 @@ is_a: MS:1001806 ! quantification object attribute id: MS:1002153 name: protein level PSM counts def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002738 ! protein-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002154 @@ -14310,59 +14494,58 @@ is_a: MS:1001861 ! quantification data processing id: MS:1002212 name: IPTL quantitation analysis def: "Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI, PMID:19655813] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002213 name: PAnalyzer:conclusive protein def: "A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002214 name: PAnalyzer:indistinguishable protein def: "A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002215 name: PAnalyzer:non-conclusive protein def: "A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002216 name: PAnalyzer:ambiguous group member def: "A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001600 ! protein inference confidence category +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002217 name: decoy peptide def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002218 name: percent collision energy ramp start def: "Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000138 ! normalized collision energy relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002219 name: percent collision energy ramp end def: "Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000138 ! normalized collision energy relationship: has_units UO:0000187 ! percent +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002220 @@ -14388,15 +14571,15 @@ relationship: part_of MS:1000908 ! transition id: MS:1002223 name: precursor ion detection probability def: "Probability of detecting precursor when parent protein is present." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002224 name: product ion detection probability def: "Probability of detecting product ion when precursor ion is present." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002225 @@ -14422,29 +14605,29 @@ relationship: has_units MS:1000905 ! percent of base peak times 100 id: MS:1002227 name: number of product ion observations def: "The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002228 name: number of precursor ion observations def: "The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002222 ! SRM transition attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002229 name: ProteomeDiscoverer:Mascot:Significance Middle def: "Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002230 name: ProteomeDiscoverer:Mascot:Significance High def: "Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002231 @@ -14463,31 +14646,31 @@ relationship: has_regexp MS:1002231 ! regular expressions for a GUID id: MS:1002233 name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained def: "Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002234 name: selected precursor m/z def: "Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI:PI] synonym: "selected ion m/z" RELATED [] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002235 name: ProteoGrouper:PDH score def: "A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002236 name: ProteoGrouper:PAG score def: "A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002237 @@ -14559,22 +14742,22 @@ is_a: MS:1002237 ! mzidLib id: MS:1002248 name: SEQUEST:spscore def: "The SEQUEST result 'SpScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002249 name: SEQUEST:sprank def: "The SEQUEST result 'SpRank'." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002250 name: SEQUEST:deltacnstar def: "The SEQUEST result 'DeltaCnStar'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002251 @@ -14586,65 +14769,65 @@ is_a: MS:1001456 ! analysis software id: MS:1002252 name: Comet:xcorr def: "The Comet result 'XCorr'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002253 name: Comet:deltacn def: "The Comet result 'DeltaCn'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002254 name: Comet:deltacnstar def: "The Comet result 'DeltaCnStar'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002255 name: Comet:spscore def: "The Comet result 'SpScore'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002256 name: Comet:sprank def: "The Comet result 'SpRank'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002257 name: Comet:expectation value def: "The Comet result 'Expectation value'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001153 ! search engine specific score +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002258 name: Comet:matched ions def: "The Comet result 'Matched Ions'." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002259 name: Comet:total ions def: "The Comet result 'Total Ions'." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002260 name: PSM:FDR threshold def: "False-discovery rate threshold for peptide-spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002483 ! PSM-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002261 @@ -14656,67 +14839,67 @@ is_a: MS:1001456 ! analysis software id: MS:1002262 name: Byonic:Score def: "The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002263 name: Byonic:Delta Score def: "The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002264 name: Byonic:DeltaMod Score def: "The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002265 name: Byonic:PEP def: "Byonic posterior error probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002266 name: Byonic:Peptide LogProb def: "The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002267 name: Byonic:Protein LogProb def: "The log p-value of the protein." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002268 name: Byonic:Best LogProb def: "Best (most negative) log p-value of an individual PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002269 name: Byonic:Best Score def: "Best (largest) Byonic score of a PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002270 @@ -14740,13 +14923,13 @@ is_a: MS:1002270 ! chromatography separation id: MS:1002273 name: detector potential def: "Detector potential difference in volts." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000481 ! detector attribute relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002274 -name: SQ Detector 2 +name: SQ Detector 2 def: "Waters quadrupole based SQ Detector 2." [PSI:MS] is_a: MS:1000126 ! Waters instrument model @@ -14834,6 +15017,7 @@ is_a: MS:1002286 ! Trans-Proteomic Pipeline software id: MS:1002288 name: iProphet def: "A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204] +synonym: "InterProphet" EXACT [] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] @@ -14924,8 +15108,8 @@ is_a: MS:1000560 ! mass spectrometer file format id: MS:1002303 name: Bruker Container nativeID format def: "Native identifier (UUID)." [PSI:MS] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000767 ! native spectrum identifier format +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002304 @@ -14961,25 +15145,25 @@ is_a: MS:1000026 ! detector type id: MS:1002309 name: Byonic: Peptide AbsLogProb def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002310 name: Byonic: Protein AbsLogProb def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002311 name: Byonic: Peptide AbsLogProb2D def: "The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002312 @@ -15009,117 +15193,117 @@ is_a: MS:1001405 ! spectrum identification result details id: MS:1002316 name: ProteomeDiscoverer:Amanda:high confidence threshold def: "Strict confidence probability score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002317 name: ProteomeDiscoverer:Amanda:middle confidence threshold def: "Relaxed confidence probability score." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002318 name: ProteomeDiscoverer:automatic workload def: "Flag indicating automatic estimation of the workload level." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002319 name: Amanda:AmandaScore def: "The Amanda score of the scoring function for a PSM." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002320 name: ProteomeDiscoverer:max differential modifications def: "Maximum dynamic modifications per PSM." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002321 name: ProteomeDiscoverer:max equal modifications def: "Maximum equal modifications per PSM." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002322 name: ProteomeDiscoverer:min peptide length def: "Minimum peptide length." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002323 name: ProteomeDiscoverer:max peptide length def: "Maximum peptide length." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002324 name: ProteomeDiscoverer:max number neutral loss def: "Maximum number of same neutral losses." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002325 name: ProteomeDiscoverer:max number neutral loss modifications def: "Max number of same neutral losses of modifications." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002326 name: ProteomeDiscoverer:use flanking ions def: "Flag for usage of flanking ions." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002327 name: ProteomeDiscoverer:max number of same modifs def: "The maximum number of possible equal modifications per PSM." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002328 name: ProteomeDiscoverer:perform deisotoping def: "Defines whether a simple deisotoping shall be performed." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002329 name: ProteomeDiscoverer:ion settings def: "Specifies the fragment ions and neutral losses that are calculated." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002330 name: ProteomeDiscoverer:3. Static Modification def: "OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002331 name: ProteomeDiscoverer:5. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002332 @@ -15138,14 +15322,12 @@ id: MS:1002334 name: ProCon def: "Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML." [PSI:PI, http://www.medizinisches-proteom-center.de/procon] is_a: MS:1002333 ! conversion software -is_a: MS:1001457 ! data processing software [Term] id: MS:1002335 name: PRIDE Converter2 def: "Java software designed to convert one of several proteomics identification results formats into PRIDE XML." [PMID:22949509] is_a: MS:1002333 ! conversion software -is_a: MS:1001457 ! data processing software [Term] id: MS:1002336 @@ -15163,30 +15345,30 @@ is_a: MS:1001456 ! analysis software id: MS:1002338 name: Andromeda:score def: "The probability based score of the Andromeda search engine." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002339 name: site:global FDR def: "Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002340 name: ProteomeXchange project tag def: "Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002341 name: second-pass peptide identification def: "A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002342 @@ -15199,7 +15381,7 @@ is_a: MS:1001457 ! data processing software id: MS:1002343 name: ion stability type def: "OBSOLETE Stability type of the ion." [PSI:PI] -comment: This child of the former purgatory term ion? was made obsolete. +comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] @@ -15214,6 +15396,7 @@ id: MS:1002345 name: PSM-level attribute def: "Attribute of a single peptide-spectrum match." [PSI:PI] is_a: MS:1002694 ! single identification result attribute +relationship: part_of MS:1003301 ! peptide-spectrum match [Term] id: MS:1002346 @@ -15243,67 +15426,67 @@ is_a: MS:1002304 ! domain range id: MS:1002350 name: PSM-level global FDR def: "Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002701 ! PSM-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002351 name: PSM-level local FDR def: "Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002352 name: PSM-level p-value def: "Estimation of the p-value for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002353 name: PSM-level e-value def: "Estimation of the e-value for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002354 name: PSM-level q-value def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002355 name: PSM-level FDRScore def: "mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002356 name: PSM-level combined FDRScore def: "mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002357 name: PSM-level probability def: "Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002358 @@ -15315,35 +15498,35 @@ is_a: MS:1001092 ! peptide sequence-level identification statistic id: MS:1002359 name: peptide sequence-level local FDR def: "Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002360 name: distinct peptide-level FDRScore -def: "mzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +def: "MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002361 name: distinct peptide-level combined FDRScore def: "Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002362 name: peptide sequence-level probability def: "Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002363 @@ -15355,32 +15538,32 @@ is_a: MS:1001116 ! single protein identification statistic id: MS:1002364 name: protein-level local FDR def: "Estimation of the local false discovery rate of proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002365 name: FDRScore for proteins -def: "mzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002366 name: combined FDRScore for proteins -def: "mzidLibrary Combined FDRScore for proteins." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002367 name: probability for proteins def: "Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002368 @@ -15392,91 +15575,91 @@ is_a: MS:1002348 ! protein group-level identification statistic id: MS:1002369 name: protein group-level global FDR def: "Estimation of the global false discovery rate of protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002706 ! protein group-level result list statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002370 name: protein group-level local FDR def: "Estimation of the local false discovery rate of protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002348 ! protein group-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002371 name: protein group-level p-value def: "Estimation of the p-value for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002372 name: protein group-level e-value def: "Estimation of the e-value for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002373 name: protein group-level q-value def: "Estimation of the q-value for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002374 name: protein group-level FDRScore def: "mzidLibrary FDRScore for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002375 name: protein group-level combined FDRScore def: "mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002376 name: protein group-level probability def: "Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002377 name: ProteomeDiscoverer:Relaxed Score Threshold def: "Specifies the threshold value for relaxed scoring." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002378 name: ProteomeDiscoverer:Strict Score Threshold def: "Specifies the threshold value for strict scoring." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002379 name: ProteomeDiscoverer:Peptide Without Protein Cut Off Score def: "Cut off score for storing peptides that do not belong to a protein." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002380 name: false localization rate def: "Estimation of the false localization rate for modification site assignment." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002381 @@ -15525,7 +15708,6 @@ name: PIA def: "PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia] is_a: MS:1002414 ! postprocessing software is_a: MS:1001456 ! analysis software -is_a: MS:1001457 ! data processing software [Term] id: MS:1002388 @@ -15544,79 +15726,79 @@ is_a: MS:1001302 ! search engine specific input parameter id: MS:1002390 name: PIA:FDRScore calculated def: "Indicates whether the FDR score was calculated for the input file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002391 name: PIA:Combined FDRScore calculated def: "Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002392 name: PIA:PSM sets created def: "Indicates whether PSM sets were created." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002393 name: PIA:used top identifications for FDR def: "The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1002394 name: PIA:protein score def: "The score given to a protein by any protein inference." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002395 name: PIA:protein inference def: "The used algorithm for the protein inference using PIA." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002396 name: PIA:protein inference filter def: "A filter used by PIA for the protein inference." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002397 name: PIA:protein inference scoring def: "The used scoring method for the protein inference using PIA." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002398 name: PIA:protein inference used score def: "The used base score for the protein inference using PIA." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002399 name: PIA:protein inference used PSMs def: "The method to determine the PSMs used for scoring by the protein inference." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002400 name: PIA:filter def: "A filter used for the report generation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002389 ! PIA workflow parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002401 @@ -15640,8 +15822,10 @@ is_a: MS:1001101 ! protein group or subset relationship id: MS:1002404 name: count of identified proteins def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002704 ! protein-level result list attribute +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002405 @@ -15653,22 +15837,22 @@ is_a: MS:1002699 ! result list attribute id: MS:1002406 name: count of identified clusters def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002405 ! protein group-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002407 name: cluster identifier def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002698 ! protein cluster identification attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002408 name: number of distinct protein sequences def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002405 ! protein group-level result list attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002409 @@ -15693,15 +15877,15 @@ is_a: MS:1002128 ! method file format id: MS:1002412 name: total XIC area def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002413 name: product background def: "The background area for the quantified transition." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002414 @@ -15713,8 +15897,8 @@ is_a: MS:1001457 ! data processing software id: MS:1002415 name: protein group passes threshold def: "A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002346 ! protein group-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002416 @@ -15744,8 +15928,8 @@ is_a: MS:1000494 ! Thermo Scientific instrument model id: MS:1002420 name: PASSEL experiment URI def: "URI that allows access to a PASSEL experiment." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002421 @@ -15757,71 +15941,71 @@ is_a: MS:1001302 ! search engine specific input parameter id: MS:1002422 name: Paragon: sample type def: "The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002423 name: Paragon: cysteine alkylation def: "The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002424 name: Paragon: instrument setting def: "The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002425 name: Paragon: search effort def: "The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002426 name: Paragon: ID focus def: "A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002427 name: Paragon: FDR analysis def: "The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002428 name: Paragon: quantitation def: "The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002429 name: Paragon: background correction def: "The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002430 name: Paragon: bias correction def: "The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002431 name: Paragon: channel to use as denominator in ratios def: "The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002432 @@ -15833,36 +16017,36 @@ is_a: MS:1001249 ! search input details id: MS:1002433 name: Paragon: modified data dictionary or parameter translation def: "This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002432 ! search engine specific input metadata +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002434 name: number of spectra searched def: "Number of spectra in a search." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001249 ! search input details +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002435 name: data processing start time def: "The time that a data processing action was started." [PSI:MS] -xref: value-type:xsd\:date "The allowed value-type for this CV term." is_a: MS:1000630 ! data processing parameter +relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term [Term] id: MS:1002436 name: Paragon: digestion def: "The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001249 ! search input details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002437 name: number of decoy sequences def: "The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI] -xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001011 ! search database details +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1002438 @@ -15922,22 +16106,22 @@ is_a: MS:1000490 ! Agilent instrument model id: MS:1002447 name: Paragon:special factor def: "The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002421 ! Paragon input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002448 name: PEAKS:inChorusPeptideScore def: "The PEAKS inChorus peptide score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002449 name: PEAKS:inChorusProteinScore def: "The PEAKS inChorus protein score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002450 @@ -16052,51 +16236,51 @@ is_a: MS:1002701 ! PSM-level result list statistic id: MS:1002466 name: PeptideShaker PSM score def: "The probability based PeptideShaker PSM score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002467 name: PeptideShaker PSM confidence def: "The probability based PeptideShaker PSM confidence." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002468 name: PeptideShaker peptide score def: "The probability based PeptideShaker peptide score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002469 name: PeptideShaker peptide confidence def: "The probability based PeptideShaker peptide confidence." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002470 name: PeptideShaker protein group score def: "The probability based PeptideShaker protein group score." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002471 name: PeptideShaker protein group confidence def: "The probability based PeptideShaker protein group confidence." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002472 @@ -16114,34 +16298,35 @@ is_a: MS:1001249 ! search input details id: MS:1002474 name: ProteoAnnotator:non-canonical gene model score def: "The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002475 name: ProteoAnnotator:count alternative peptides def: "The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002476 name: ion mobility drift time def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute -is_a: MS:1000503 ! scan attribute +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1003254 ! peak attribute relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002477 -name: mean drift time array -def: "Array of drift times, averaged from a matrix of binned m/z and drift time values, corresponding to spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000513 ! binary data array +name: mean ion mobility drift time array +def: "Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002478 @@ -16202,15 +16387,15 @@ is_a: MS:1002572 ! protein detection statistical threshold id: MS:1002487 name: MassIVE dataset identifier def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002488 name: MassIVE dataset URI def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002489 @@ -16245,8 +16430,9 @@ is_a: MS:1002489 ! special processing [Term] id: MS:1002494 -name: cross-linking search -def: "Cross-linking search performed." [PSI:PI] +name: crosslinking search +def: "Crosslinking search performed." [PSI:PI] +synonym: "cross-linking search" EXACT [] is_a: MS:1002489 ! special processing [Term] @@ -16285,8 +16471,8 @@ is_obsolete: true id: MS:1002500 name: peptide passes threshold def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002501 @@ -16310,13 +16496,13 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute id: MS:1002504 name: modification index def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001055 ! modification parameters +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002505 name: regular expression for modification localization scoring -def: "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})." [PSI:PI] +def: "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] @@ -16329,50 +16515,55 @@ is_a: MS:1001055 ! modification parameters id: MS:1002507 name: modification rescoring:false localization rate def: "Mod position score: false localization rate." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002506 ! modification position score relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002508 -name: cross-linking attribute -def: "Cross-linking attribute." [PSI:PI] +name: crosslinking attribute +def: "Crosslinking attribute." [PSI:PI] +synonym: "cross-linking attribute" EXACT [] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002509 -name: cross-link donor -def: "The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002508 ! cross-linking attribute +name: crosslink donor +def: "The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] +synonym: "cross-link donor" EXACT [] +is_a: MS:1002508 ! crosslinking attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002510 -name: cross-link acceptor -def: "Cross-linking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002508 ! cross-linking attribute +name: crosslink acceptor +def: "Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] +synonym: "cross-link acceptor" EXACT [] +is_a: MS:1002508 ! crosslinking attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002511 -name: cross-link spectrum identification item -def: "Cross-linked spectrum identification item." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." -is_a: MS:1002508 ! cross-linking attribute +name: crosslink spectrum identification item +def: "Crosslinked spectrum identification item." [PSI:PI] +synonym: "cross-link spectrum identification item" EXACT [] +is_a: MS:1002508 ! crosslinking attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002512 -name: cross-linking score -def: "Cross-linking scoring value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +name: crosslinking score +def: "Crosslinking scoring value." [PSI:PI] +synonym: "cross-linking score" EXACT [] is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002513 -name: molecules per cell +name: molecules per cell def: "The absolute abundance of protein in a cell." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002514 @@ -16384,43 +16575,43 @@ is_a: MS:1001833 ! quantitation analysis summary id: MS:1002515 name: internal peptide reference used def: "States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001832 ! quantitation software comment or customizations +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002516 name: internal protein reference used def: "States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001832 ! quantitation software comment or customizations +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002517 name: internal reference abundance def: "The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002518 name: Progenesis:protein group normalised abundance def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002739 ! protein group-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002519 name: Progenesis:protein group raw abundance def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002739 ! protein group-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002520 name: peptide group ID def: "Peptide group identifier for peptide-level stats." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002521 @@ -16432,8 +16623,8 @@ is_a: MS:1000857 ! run attribute id: MS:1002522 name: ProteomeDiscoverer:1. Static Terminal Modification def: "Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002523 @@ -16510,91 +16701,91 @@ is_a: MS:1000121 ! SCIEX instrument model id: MS:1002534 name: ProLuCID:xcorr def: "The ProLuCID result 'XCorr'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002535 name: ProLuCID:deltacn def: "The ProLuCID result 'DeltaCn'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002536 name: D-Score -def: "D-Score for PTM site location at the PSM-level." [DOI:10.1002/pmic.201200408, PMID:23307401] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "D-Score for PTM site location at the PSM-level." [PMID:23307401] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002537 name: MD-Score -def: "MD-Score for PTM site location at the PSM-level." [DOI:10.1074/mcp.M110.003830–1, PMID:21057138] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002538 name: PTM localization confidence metric def: "Localization confidence metric for a post translational modification (PTM)." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002539 name: PeptideShaker PTM confidence type def: "PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002538 ! PTM localization confidence metric +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002540 name: PeptideShaker PSM confidence type def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002347 ! PSM-level identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002541 name: PeptideShaker peptide confidence type def: "PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002542 name: PeptideShaker protein confidence type def: "PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein identification statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002543 name: xiFDR -def: "Target/Decoy based FDR estimation for cross-linking peptide-identifications." [PSI:PI] +def: "Target/Decoy based FDR estimation for crosslinking peptide-identifications." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002544 name: xi -def: "Search engine for cross-linked peptides." [PSI:PI] +def: "Search engine for crosslinked peptides." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002545 name: xi:score def: "The xi result 'Score'." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002546 -name: Skyline mzQuantML converter +name: Skyline mzQuantML converter def: "A software package to convert Skyline report to mzQuantML." [PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software @@ -16608,7 +16799,7 @@ is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002548 name: distributed normalized spectral abundance factor -def: "A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708] +def: "A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708] is_a: MS:1001805 ! quantification datatype [Term] @@ -16621,41 +16812,41 @@ is_a: MS:1002689 ! PTM localization single result statistic id: MS:1002550 name: peptide:phosphoRS score def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002551 name: peptide:Ascore def: "A-score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002552 name: peptide:H-Score def: "H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002553 name: peptide:D-Score def: "D-Score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002554 name: peptide:MD-Score def: "MD-Score for PTM site location at the peptide-level." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002555 @@ -16667,113 +16858,113 @@ is_a: MS:1001405 ! spectrum identification result details id: MS:1002556 name: Ascore threshold def: "Threshold for Ascore PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002557 name: D-Score threshold def: "Threshold for D-score PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002558 name: MD-Score threshold def: "Threshold for MD-score PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002559 name: H-Score threshold def: "Threshold for H-score PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002560 name: DeBunker:score threshold def: "Threshold for DeBunker PTM site location score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002561 name: Mascot:PTM site assignment confidence threshold def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002562 name: MSQuant:PTM-score threshold def: "Threshold for MSQuant:PTM-score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002563 name: MaxQuant:PTM Score threshold def: "Threshold for MaxQuant:PTM Score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002564 name: MaxQuant:P-site localization probability threshold def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002565 name: MaxQuant:PTM Delta Score threshold def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002566 name: MaxQuant:Phospho (STY) Probabilities threshold def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002567 name: phosphoRS score threshold def: "Threshold for phosphoRS score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002568 name: phosphoRS site probability threshold def: "Threshold for phosphoRS site probability." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002569 name: ProteomeDiscoverer:Number of Spectra Processed At Once def: "Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002101 ! ProteomeDiscoverer input parameter +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002570 name: sequence multiply subsumable protein def: "A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002571 name: spectrum multiply subsumable protein def: "A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001101 ! protein group or subset relationship +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002572 @@ -16940,9 +17131,9 @@ is_a: MS:1001456 ! analysis software [Term] id: MS:1002599 name: splash key -def: "The Splash, is an unique identifier for Spectra, as the InChI Key is an unique identifier for chemical compounds." [http://splash.fiehnlab.ucdavis.edu/] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002600 @@ -16959,7 +17150,7 @@ is_a: MS:1000914 ! tab delimited text format [Term] id: MS:1002602 -name: quantification reagent +name: sample label def: "Reagent used in labeled quantification methods." [PSI:PI] is_a: MS:1002111 ! assay label attribute is_a: MS:1000548 ! sample attribute @@ -16968,7 +17159,7 @@ is_a: MS:1000548 ! sample attribute id: MS:1002603 name: ICAT reagent def: "Isotope coded affinity tag reagent." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002604 @@ -16986,7 +17177,7 @@ is_a: MS:1002603 ! ICAT reagent id: MS:1002606 name: ICPL reagent def: "Isotope coded protein labeling reagent." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002607 @@ -17016,7 +17207,7 @@ is_a: MS:1002606 ! ICPL reagent id: MS:1002611 name: SILAC reagent def: "Stable isotope labeling with amino acids in cell culture reagent." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002612 @@ -17040,7 +17231,7 @@ is_a: MS:1002611 ! SILAC reagent id: MS:1002615 name: TMT reagent def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002616 @@ -17082,7 +17273,7 @@ is_a: MS:1002615 ! TMT reagent id: MS:1002622 name: iTRAQ reagent def: "Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002623 @@ -17134,24 +17325,24 @@ is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002631 -name: Electron-Transfer/Higher-Energy Collision Dissociation (EThcD) -def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI] +name: electron-transfer/higher-energy collision dissociation +def: "Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI] synonym: "EThcD" EXACT [] -is_a: MS:1000044 ! dissociation method +is_a: MS:1003181 ! combined dissociation method [Term] id: MS:1002632 name: jPOST dataset identifier def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002633 name: jPOST dataset URI def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002634 @@ -17175,59 +17366,59 @@ is_a: MS:1001105 ! peptide sequence-level identification attribute id: MS:1002637 name: chromosome name def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002638 name: chromosome strand def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002639 name: peptide start on chromosome def: "OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI] comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute is_obsolete: true +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002640 name: peptide end on chromosome def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002641 name: peptide exon count def: "The number of exons to which the peptide has been mapped." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002642 name: peptide exon nucleotide sizes def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002643 name: peptide start positions on chromosome def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002644 name: genome reference version def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002636 ! proteogenomics attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002645 @@ -17241,90 +17432,90 @@ id: MS:1002646 name: native spectrum identifier format, combined spectra def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI] synonym: "nativeID format, combined spectra" EXACT [] -relationship: part_of MS:1000577 ! raw data file +relationship: part_of MS:1000577 ! source data file [Term] id: MS:1002647 name: Thermo nativeID format, combined spectra def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002648 name: Waters nativeID format, combined spectra def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002649 name: WIFF nativeID format, combined spectra def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002650 name: Bruker/Agilent YEP nativeID format, combined spectra def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002651 name: Bruker BAF nativeID format, combined spectra def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002652 name: Bruker FID nativeID format, combined spectra def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: The nativeID must be the same as the source file ID. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002653 name: multiple peak list nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002654 name: single peak list nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002655 name: scan number only nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002656 name: spectrum identifier nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion from mzData. The spectrum id attribute is referenced. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002657 name: mzML unique identifier, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: A unique identifier of a spectrum stored in an mzML file. -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002658 @@ -17336,7 +17527,6 @@ relationship: part_of MS:1001000 ! spectrum interpretation id: MS:1002659 name: UniProtKB text sequence format def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI] -xref: SWO:http://edamontology.org/format_2187 is_a: MS:1001347 ! database file formats [Term] @@ -17355,30 +17545,32 @@ is_a: MS:1001456 ! analysis software id: MS:1002662 name: Morpheus:Morpheus score def: "Morpheus score for PSMs." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002663 name: Morpheus:summed Morpheus score def: "Summed Morpheus score for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002664 -name: interaction score derived from cross-linking -def: "Parent term for interaction scores derived from cross-linking." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002675 ! cross-linking result details -relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) +name: interaction score derived from crosslinking +def: "Parent term for interaction scores derived from crosslinking." [PSI:PI] +synonym: "interaction score derived from cross-linking" EXACT [] +is_a: MS:1002675 ! crosslinking result details +relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002665 -name: regular expression for interaction scores derived from cross-linking -def: "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))." [PSI:PI] +name: regular expression for interaction scores derived from crosslinking +def: "((?[0-9]+)[.](?[a|b]):(?[0-9]+|null):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?):(?true|false))|(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?)" [PSI:PI] +synonym: "regular expression for interaction scores derived from cross-linking" EXACT [] is_a: MS:1002479 ! regular expression [Term] @@ -17397,29 +17589,29 @@ is_a: MS:1001536 ! Bruker Daltonics micrOTOF series id: MS:1002668 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002669 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002670 name: frag: TMT reporter ion def: "Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002671 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002672 @@ -17441,27 +17633,28 @@ is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002675 -name: cross-linking result details -def: "This subsection describes terms which can describe details of cross-linking results." [PSI:PI] +name: crosslinking result details +def: "This subsection describes terms which can describe details of crosslinking results." [PSI:PI] +synonym: "cross-linking result details" EXACT [] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1002676 name: protein-pair-level global FDR -def: "Estimation of the global false discovery rate of proteins-pairs in cross-linking experiments." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002664 ! interaction score derived from cross-linking -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) +def: "Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments." [PSI:PI] +is_a: MS:1002664 ! interaction score derived from crosslinking +relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive +relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002677 name: residue-pair-level global FDR -def: "Estimation of the global false discovery rate of residue-pairs in cross-linking experiments." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." -is_a: MS:1002664 ! interaction score derived from cross-linking -relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive -relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})) +def: "Estimation of the global false discovery rate of residue-pairs in crosslinking experiments." [PSI:PI] +is_a: MS:1002664 ! interaction score derived from crosslinking +relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive +relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002678 @@ -17479,66 +17672,66 @@ is_a: MS:1000133 ! collision-induced dissociation id: MS:1002680 name: supplemental collision energy def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002681 name: OpenXQuest:combined score -def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +def: "OpenXQuest's combined score for a crosslink spectrum match." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002682 name: OpenXQuest:xcorr xlink -def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." +def: "OpenXQuest's cross-correlation of crosslinked ions subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002683 name: OpenXQuest:xcorr common def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002684 name: OpenXQuest:match-odds def: "OpenXQuest's match-odds subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002685 name: OpenXQuest:intsum def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002686 name: OpenXQuest:wTIC def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002687 @@ -17654,6 +17847,59 @@ name: protein group-level result list statistic def: "Attrbiute of an entire list of protein groups." [PSI:PI] is_a: MS:1002405 ! protein group-level result list attribute +[Term] +id: MS:1002707 +name: (?=[KR]) +def: "Regular expression for LysargiNase." [PSI:PI] +is_a: MS:1001180 ! Cleavage agent regular expression + +[Term] +id: MS:1002708 +name: LysargiNase +def: "Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues." [PMID:25419962] +synonym: "Tryp-N" EXACT [] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1002707 ! (?=[KR]) + +[Term] +id: MS:1002709 +name: compound data type +def: "A data type representing more than a single value." [] + +[Term] +id: MS:1002710 +name: list of type +def: "A data type defining a list of values of a single type." [] +is_a: MS:1002709 ! compound data type + +[Term] +id: MS:1002711 +name: list of strings +def: "A list of xsd:string." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002712 +name: list of integers +def: "A list of xsd:integer." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002713 +name: list of floats +def: "A list of xsd:float." [] +is_a: MS:1002710 ! list of type +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002714 +name: FLASHDeconv +def: "Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics." [DOI:10.1016/j.cels.2020.01.003] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + [Term] id: MS:1002719 name: Pegasus BT @@ -17670,41 +17916,41 @@ is_a: MS:1001456 ! analysis software id: MS:1002721 name: MSPathFinder:SpecEValue def: "MSPathFinder spectral E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002722 name: MSPathFinder:EValue def: "MSPathFinder E-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002723 name: MSPathFinder:QValue def: "MSPathFinder Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002724 name: MSPathFinder:PepQValue def: "MSPathFinder peptide-level Q-value." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002725 name: MSPathFinder:RawScore def: "MSPathFinder raw score." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002726 @@ -17726,7 +17972,7 @@ is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002729 -name: Xevo G2 XS Tof +name: Xevo G2-XS Tof def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model @@ -17752,15 +17998,15 @@ is_a: MS:1000494 ! Thermo Scientific instrument model id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] -xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002737 ! peptide-level quantification datatype +relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002735 @@ -17819,7 +18065,7 @@ def: "A data array of parallel, independent m/z values for a sampling of noise a xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array -relationship: has_units MS:1000040 ! m/z +relationship: has_units MS:1000040 ! m/z [Term] id: MS:1002744 @@ -17860,13 +18106,13 @@ is_a: MS:1000572 ! binary data compression type id: MS:1002749 name: Mascot:IntegratedSpectralLibrarySearch def: "Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI] -xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002750 name: NIST MSPepSearch -def: "Search tool of the NIST (National Institute of Standrads and Technology) for spectral library searches." [PSI:PI] +def: "Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] @@ -17905,49 +18151,42 @@ is_a: MS:1001080 ! search type id: MS:1002756 name: iodoTMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002757 name: glyco-TMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, PMID:22455665] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002758 name: aminoxyTMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, PMID:25337643] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002759 name: hydrazideTMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, PMID:25337643] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002760 name: iTRAQH quantitation analysis def: "Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow." [PSI:PI, PMID:22926130] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002761 name: DiART quantitation analysis def: "Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, PMID:20715779] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002762 name: DiLeu quantitation analysis def: "Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779] -is_a: MS:1001833 ! quantitation analysis summary is_a: MS:1002009 ! isobaric label quantitation analysis [Term] @@ -18002,7 +18241,7 @@ is_a: MS:1002615 ! TMT reagent id: MS:1002771 name: DiART reagent def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002772 @@ -18044,7 +18283,7 @@ is_a: MS:1002771 ! DiART reagent id: MS:1002778 name: DiLeu reagent def: "Dimethyl leucine labeling reagent." [PSI:PI] -is_a: MS:1002602 ! quantification reagent +is_a: MS:1002602 ! sample label [Term] id: MS:1002779 @@ -18211,8 +18450,8 @@ is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002806 name: ion -def: "An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] -relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology +def: "Molecular entity having a net positive or negative electric charge." [PSI:MS] +is_a: MS:1000881 ! molecular entity [Term] id: MS:1002807 @@ -18229,22 +18468,23 @@ is_a: MS:1000353 ! adduct ion [Term] id: MS:1002809 name: adduct ion attribute -def: "Attribute describing an adduct formation." [PSI:PI] -is_a: MS:1000547 ! object attribute +def: "Nonphysical characteristic attributed to an adduct ion." [PSI:MS] +relationship: part_of MS:1000353 ! adduct ion [Term] id: MS:1002810 -name: adduct ion mass -def: "Mass of an adduct formation specified by the given value." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002809 ! adduct ion attribute +name: adduct ion X m/z +def: "Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS] +is_a: MS:1003056 ! adduct ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000040 ! m/z [Term] id: MS:1002811 name: adduct ion isotope -def: "Isotope of the matrix molecule M of an adduct formation." [PMID:18790129] -xref: value-type:xsd\:string "The allowed value-type for this CV term." -is_a: MS:1002809 ! adduct ion attribute +def: "Isotope of the matrix molecule M of an adduct formation." [PSI:MS] +is_a: MS:1003056 ! adduct ion property +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002812 @@ -18255,10 +18495,10 @@ is_a: MS:1002479 ! regular expression [Term] id: MS:1002813 name: adduct ion formula -def: "Adduct formation formula specified by the given value." [PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] -xref: value-type:xsd\:string "The allowed value-type for this CV term." +def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS] is_a: MS:1002809 ! adduct ion attribute relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002814 @@ -18271,20 +18511,20 @@ is_a: UO:0000000 ! unit id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute -is_a: MS:1000503 ! scan attribute -relationship: has_units MS:1002814 ! "volt-second per square centimeter" +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002816 name: mean ion mobility array -def: "Array of drift times or inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] -xref: value-type:xsd\:float "The allowed value-type for this CV term." -is_a: MS:1000513 ! binary data array +def: "Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second -relationship: has_units MS:1002814 ! "volt-second per square centimeter" +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002817 @@ -18302,27 +18542,27 @@ is_a: MS:1000767 ! native spectrum identifier format id: MS:1002819 name: Bruker TDF nativeID format, combined spectra def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002820 name: M+H ion -def: "M+H ion from positive ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] +def: "Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton." [PSI:MS] property_value: ionMass: "M + 1.007276" xsd:string is_a: MS:1002807 ! positive mode adduct ion [Term] id: MS:1002821 name: M-H ion -def: "M-H ion from negative ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] +def: "Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M." [PSI:MS] property_value: ionMass: "M - 1.007276" xsd:string is_a: MS:1002808 ! negative mode adduct ion [Term] id: MS:1002822 name: OpenMS file format -def: "File format developed by the OpenMS team." [PMID: 27575624] +def: "File format developed by the OpenMS team." [PMID:27575624] is_a: MS:1001459 ! file format [Term] @@ -18353,45 +18593,45 @@ is_a: MS:1001456 ! analysis software id: MS:1002827 name: MetaMorpheus:score def: "MetaMorpheus score for PSMs." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002828 name: MetaMorpheus:protein score def: "MetaMorpheus score for protein groups." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002829 name: XCMS:into def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002830 name: XCMS:intf def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002831 name: XCMS:maxo def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002832 name: XCMS:area def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] -xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002735 ! feature-level quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002833 @@ -18403,8 +18643,8 @@ is_a: MS:1000857 ! run attribute id: MS:1002834 name: ProteomeDiscoverer:Delta Score def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] -xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002835 @@ -18416,12 +18656,6491 @@ is_a: MS:1000494 ! Thermo Scientific instrument model id: MS:1002836 name: iProX dataset identifier def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002837 name: iProX dataset URI def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] -xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002838 +name: mzMLb format +def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002839 +name: Conversion to mzMLb +def: "Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1002840 +name: external reference data +def: "Data belonging to an external reference." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1002841 +name: external HDF5 dataset +def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray." [PSI:PI] +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002842 +name: external offset +def: "The position in the external data where the array begins." [PSI:PI] +relationship: has_units UO:0000189 ! Count +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002843 +name: external array length +def: "Describes how many fields an array contains." [PSI:PI] +relationship: has_units UO:0000189 ! Count +is_a: MS:1002840 ! external reference data +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002844 +name: Experiment additional parameter +def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] +is_a: MS:1001458 ! spectrum generation information + +[Term] +id: MS:1002845 +name: Associated file URI +def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002846 +name: Associated raw file URI +def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002847 +name: ProteomeCentral dataset URI +def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002848 +name: Result file URI +def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002849 +name: Search engine output file URI +def: "URI of one search engine output file associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002850 +name: Peak list file URI +def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002851 +name: Other type file URI +def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002852 +name: Dataset FTP location +def: "FTP location of one entire PX data set." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002853 +name: Dataset with no associated published manuscript +def: "A dataset which does not have an associated published manuscript." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002854 +name: Peer-reviewed dataset +def: "Dataset has been peer-reviewed somehow." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002855 +name: Non peer-reviewed dataset +def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002856 +name: Supported dataset by repository +def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002857 +name: Unsupported dataset by repository +def: "Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002858 +name: Dataset with its publication pending +def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002859 +name: Additional associated raw file URI +def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002860 +name: Gel image file URI +def: "URI of one gel image file associated to one PX submission." [PSI:PI] +is_a: MS:1002845 ! Associated file URI +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002861 +name: Reprocessed complete dataset +def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002862 +name: Reprocessed subset dataset +def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002863 +name: Data derived from previous dataset +def: "One dataset is a reanalysis of previously published data." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002864 +name: No PTMs are included in the dataset +def: "No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002865 +name: Accepted manuscript +def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002866 +name: Reference +def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002867 +name: Experimental information has been refined since this experiment was originally made publicly available +def: "This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002868 +name: Original data +def: "One dataset is not a reanalysis of previously published data." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1002869 +name: mzR +def: "Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002870 +name: MSnbase +def: "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002871 +name: CAMERA +def: "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002872 +name: Panorama Public dataset identifier +def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002873 +name: Panorama Public dataset URI +def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term + +[Term] +id: MS:1002874 +name: TSQ Altis +def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002875 +name: TSQ Quantis +def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002876 +name: TSQ 9000 +def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002877 +name: Q Exactive HF-X +def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1002878 +name: small molecule analysis software +def: "Software for the analysis of small molecules." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002879 +name: Progenesis QI +def: "Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002880 +name: Compound Discoverer +def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002881 +name: MyCompoundID +def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002882 +name: study variable average function +def: "Function used to calculate the study variable quantification value." [PSI:PI] +is_a: MS:1001184 ! search statistics + +[Term] +id: MS:1002883 +name: median +def: "Median function." [PSI:PI] +is_a: MS:1002882 ! study variable average function + +[Term] +id: MS:1002884 +name: study variable variation function +def: "Function used to calculate the study variable quantification variation value." [PSI:PI] +is_a: MS:1001184 ! search statistics + +[Term] +id: MS:1002885 +name: standard error +def: "Standard error function." [PSI:PI] +is_a: MS:1002884 ! study variable variation function + +[Term] +id: MS:1002886 +name: small molecule quantification datatype +def: "The value reported in a small molecule quantification." [PSI:PI] +is_a: MS:1001805 ! quantification datatype + +[Term] +id: MS:1002887 +name: Progenesis QI normalised abundance +def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] +is_a: MS:1002886 ! small molecule quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002888 +name: small molecule confidence measure +def: "The confidence score produced by a small molecule analysis software." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002889 +name: Progenesis MetaScope score +def: "The confidence score produced by Progenesis QI." [PSI:PI] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002890 +name: fragmentation score +def: "The fragmentation confidence score." [PSI:PI] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002891 +name: isotopic fit score +def: "The isotopic fit confidence score." [PSI:PI] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1002892 +name: ion mobility attribute +def: "An attribute describing ion mobility searches." [PSI:PI] +is_a: MS:1000503 ! scan attribute +is_a: MS:1002345 ! PSM-level attribute + +[Term] +id: MS:1002893 +name: ion mobility array +def: "Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided." [PSI:PI] +is_a: MS:1000513 ! binary data array + +[Term] +id: MS:1002894 +name: InChIKey +def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] +is_a: MS:1001405 ! spectrum identification result details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002895 +name: small molecule identification attribute +def: "Compound identification information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002896 +name: compound identification confidence level +def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] +is_a: MS:1002895 ! small molecule identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002897 +name: isotopomer peak +def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] +comment: This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. +is_a: MS:1000231 ! peak +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002898 +name: Shimadzu Biotech QTOF nativeID format +def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1002899 +name: msalign format +def: "msalign file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002900 +name: feature format +def: "TopFD feature file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002901 +name: TopPIC +def: "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002902 +name: TopFD +def: "Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002903 +name: TopMG +def: "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002904 +name: proteoform-level identification attribute +def: "Proteoform level information." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1002905 +name: proteoform-level identification statistic +def: "Identification confidence metric for a proteoform." [PSI:PI] +is_a: MS:1002904 ! proteoform-level identification attribute + +[Term] +id: MS:1002906 +name: search engine specific score for proteoforms +def: "Search engine specific proteoform scores." [PSI:PI] +is_a: MS:1002905 ! proteoform-level identification statistic + +[Term] +id: MS:1002907 +name: proteoform-level global FDR +def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002905 ! proteoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002908 +name: proteoform-level local FDR +def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002905 ! proteoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002909 +name: proteoform-level statistical threshold +def: "Estimated statistical threshold at proteoform-level." [PSI:PI] +is_a: MS:1002573 ! spectrum identification statistical threshold + +[Term] +id: MS:1002910 +name: proteoform-level global FDR threshold +def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002909 ! proteoform-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002911 +name: proteoform-level local FDR threshold +def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] +is_a: MS:1002909 ! proteoform-level statistical threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002912 +name: TopPIC input parameter +def: "Search engine input parameters specific to TopPIC." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002913 +name: TopPIC:fixed modification +def: "Fixed modifications for TopPIC searching." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter + +[Term] +id: MS:1002914 +name: TopPIC:N-term form +def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter + +[Term] +id: MS:1002915 +name: TopPIC:error tolerance +def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002916 +name: TopPIC:max shift +def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002917 +name: TopPIC:min shift +def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002918 +name: TopPIC:shift num +def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002919 +name: TopPIC:spectral cutoff type +def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002920 +name: TopPIC:spectral cutoff value +def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002921 +name: TopPIC:proteoform-level cutoff type +def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002922 +name: TopPIC:proteoform-level cutoff value +def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002923 +name: TopPIC:generating function +def: "P-value and E-value estimation using generating function." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002924 +name: TopPIC:combined spectrum number +def: "Number of combined spectra." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002925 +name: TopPIC:mod file +def: "The text file containing the information of common PTMs." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter + +[Term] +id: MS:1002926 +name: TopPIC:thread number +def: "Number of threads used in TopPIC." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002927 +name: TopPIC:use TopFD feature +def: "Proteoform identification using TopFD feature file." [PSI:PI] +is_a: MS:1002912 ! TopPIC input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002928 +name: TopPIC:spectral E-value +def: "TopPIC spectrum-level E-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002353 ! PSM-level e-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002929 +name: TopPIC:spectral FDR +def: "TopPIC spectrum-level FDR." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002351 ! PSM-level local FDR +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002930 +name: TopPIC:proteoform-level FDR +def: "TopPIC proteoform-level FDR." [PSI:PI] +is_a: MS:1002908 ! proteoform-level local FDR +is_a: MS:1002906 ! search engine specific score for proteoforms +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002931 +name: TopPIC:spectral p-value +def: "TopPIC spectrum-level p-value." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1002352 ! PSM-level p-value +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002932 +name: TopPIC:MIScore +def: "Modification identification score." [PMID:27291504] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002933 +name: TopPIC:MIScore threshold +def: "TopPIC:MIScore threshold." [PSI:PI] +is_a: MS:1002555 ! PTM localization score threshold +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002934 +name: TopMG input parameter +def: "Search engine input parameters specific to TopMG." [PSI:PI] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1002935 +name: TopMG:fixed modification +def: "Fixed modifications for TopMG searching." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter + +[Term] +id: MS:1002936 +name: TopMG:N-term form +def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter + +[Term] +id: MS:1002937 +name: TopMG:error tolerance +def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002938 +name: TopMG:max shift +def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002939 +name: TopMG:spectral cutoff type +def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002940 +name: TopMG:spectral cutoff value +def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002941 +name: TopMG:proteoform-level cutoff type +def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002942 +name: TopMG:proteoform-level cutoff value +def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002943 +name: TopMG:mod file +def: "The text file containing the information of common PTMs." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter + +[Term] +id: MS:1002944 +name: TopMG:thread number +def: "Number of threads used in TopMG." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002945 +name: TopMG:use TopFD feature +def: "Proteoform identification using TopFD feature file." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002946 +name: TopMG:proteoform graph gap size +def: "Gap size in constructing proteoform graph." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002947 +name: TopMG:variable PTM number +def: "Maximum number of variable PTMs." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002948 +name: TopMG:variable PTM number in proteoform graph gap +def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1002949 +name: TopMG:use ASF-DIAGONAL +def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] +is_a: MS:1002934 ! TopMG input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1002950 +name: TopMG:spectral E-value +def: "TopMG spectrum-level E-value." [PSI:PI] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002951 +name: TopMG:spectral FDR +def: "TopMG spectrum-level FDR." [PSI:PI] +is_a: MS:1002351 ! PSM-level local FDR +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002952 +name: TopMG:proteoform-level FDR +def: "TopMG proteoform-level FDR." [PSI:PI] +is_a: MS:1002908 ! proteoform-level local FDR +is_a: MS:1002906 ! search engine specific score for proteoforms +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002953 +name: TopMG:spectral p-value +def: "TopMG spectrum-level p-value." [PSI:PI] +is_a: MS:1002352 ! PSM-level p-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002954 +name: collisional cross sectional area +def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] +is_a: MS:1000861 ! molecular entity property +is_a: MS:1000455 ! ion selection attribute +relationship: has_units UO:0000324 ! square angstrom +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002955 +name: hr-ms compound identification confidence level +def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] +is_a: MS:1002895 ! small molecule identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002956 +name: isotopic ion MS peak +def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] +is_a: MS:1000231 ! peak +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002957 +name: isotopomer MS peak +def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] +is_a: MS:1002956 ! isotopic ion MS peak +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002958 +name: isotopologue MS peak +def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] +is_a: MS:1002956 ! isotopic ion MS peak +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002959 +name: isomer +def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] +is_a: MS:1000859 ! molecule +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002960 +name: isotopomer +def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] +is_a: MS:1002959 ! isomer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002961 +name: isotopologue +def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] +is_a: MS:1002959 ! isomer +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1002962 +name: mean +def: "The arithmetic mean." [PSI:PI] +is_a: MS:1002882 ! study variable average function + +[Term] +id: MS:1002963 +name: variation coefficient +def: "The coefficient of variation." [PSI:PI] +is_a: MS:1002884 ! study variable variation function + +[Term] +id: MS:1002964 +name: lipidomics analysis software +def: "Lipidomics analysis software." [PSI:PI] +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1002965 +name: Lipid Data Analyzer +def: "Lipid Data Analyzer software for lipid quantification." [PMID:29058722] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002966 +name: chrom format +def: "The Lipid Data Analyzer native chrom format." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002967 +name: LipidHunter +def: "Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002968 +name: LipidXplorer +def: "Software for consensual cross-platform lipidomics." [PMID:22272252] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002969 +name: LipidMatch +def: "An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data." [PMID:28693421] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002970 +name: Greazy +def: "Open-source software for automated phospholipid tandem mass spectrometry identification." [PMID:27186799] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002971 +name: LipidBlast +def: "LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library." [PMID:28660581] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002972 +name: Lipid-Pro +def: "A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms." [PMID:25433698] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002973 +name: LipidFinder +def: "A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets." [PMID:28405621] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002974 +name: LipiDex +def: "An integrated software package for high-confidence lipid identification." [PMID:29705063] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002975 +name: LIQUID +def: "An-open source software for identifying lipids in LC-MS/MS-based lipidomics data." [PMID:28158427] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002976 +name: ALEX +def: "Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1)." [PMID:24244551] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002977 +name: ALEX123 +def: "Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level." [PMID:29786091] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002978 +name: LIMSA +def: "Software tool for the quantitative analysis of mass spectrometric lipidome data." [PMID:17165823] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002979 +name: LOBSTAHS +def: "Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers." [PMID:27322848] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002980 +name: LipidQA +def: "Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species." [PMID:17720531] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002981 +name: Proline +def: "The Proline software suite for mass spectrometry based proteomics." [http://www.profiproteomics.fr/proline/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002982 +name: PepNovo +def: "PepNovo tool for de novo peptide sequencing." [PMID:15858974] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002983 +name: pNovo +def: "pNovo tool for de novo peptide sequencing and identification using HCD spectra." [PMID:20329752] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002984 +name: Novor +def: "Novor real-time peptide de novo sequencing software tool." [PMID:26122521] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002985 +name: in-gel digestion +def: "Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes." [PSI:PI] +is_a: MS:1000831 ! sample preparation + +[Term] +id: MS:1002986 +name: in-solution digestion +def: "Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes." [PSI:PI] +is_a: MS:1000831 ! sample preparation + +[Term] +id: MS:1002987 +name: IdentiPy +def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1002988 +name: IdentiPy:RHNS +def: "The IdentiPy result 'RHNS'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002989 +name: IdentiPy:hyperscore +def: "The IdentiPy result 'hyperscore'." [PSI:PI] +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002990 +name: ms_deisotope +def: "ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra." [https://github.com/mobiusklein/ms_deisotope] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1002991 +name: python-psims +def: "python-psims, a library for generating mzML and mzIdentML." [https://github.com/mobiusklein/psims] +is_a: MS:1002333 ! conversion software + +[Term] +id: MS:1002995 +name: Andromeda:PEP +def: "Posterior error probability of the best identified peptide of the Andromeda search engine." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1002996 +name: Andromeda:apl file format +def: "Peak list file format of the Andromeda search engine." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1002997 +name: ProteomeXchange dataset identifier reanalysis number +def: "Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1002998 +name: LCMS-9030 +def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1002999 +name: LCMS-8060 +def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003000 +name: LCMS-8050 +def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003001 +name: LCMS-8045 +def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003002 +name: LCMS-8040 +def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003003 +name: LCMS-2020 +def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003004 +name: maXis II +def: "Bruker Daltonics' maXis II." [PSI:MS] +is_a: MS:1001547 ! Bruker Daltonics maXis series + +[Term] +id: MS:1003005 +name: timsTOF Pro +def: "Bruker Daltonics' timsTOF Pro." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003006 +name: mean inverse reduced ion mobility array +def: "Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003007 +name: raw ion mobility array +def: "Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003008 +name: raw inverse reduced ion mobility array +def: "Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003009 +name: Shimadzu Biotech LCD format +def: "Shimadzu Biotech LCD file format." [PSI:PI] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003010 +name: LPPtiger +def: "Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets." [PMID:29123162] +is_a: MS:1002964 ! lipidomics analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003011 +name: pFind +def: "Sequence-tag-based search engine pFind." [PMID:30295672] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003012 +name: KSDP score +def: "Kernel mass spectral dot product scoring function." [PMID:15044235] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better + +[Term] +id: MS:1003013 +name: i3tms +def: "i3-tms search engine and data-analysis software." [PSI:PI] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003014 +name: MSFragger +def: "A database search-based peptide identification tool." [PMID:28394336] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003015 +name: razor peptide +def: "Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides." [PSI:MS] +is_a: MS:1000860 ! peptide + +[Term] +id: MS:1003016 +name: ProteinProphet:peptide weight +def: "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI] +is_a: MS:1002490 ! peptide-level scoring +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003017 +name: ProteinProphet:peptide group weight +def: "Fraction of peptide evidence attributable to a group of proteins." [PSI:PI] +is_a: MS:1002490 ! peptide-level scoring +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003018 +name: Philosopher +def: "General proteomics processing toolkit for shotgun proteomics." [https://philosopher.nesvilab.org/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003019 +name: pressure chromatogram +def: "Representation of chromatographic pressure versus time." [PSI:MS] +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1003020 +name: flow rate chromatogram +def: "Representation of the chromatographic flow rate versus time." [PSI:MS] +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1003021 +name: Fixed modification +def: "Post-translational modification which is assumed to be present at each instance of a residue type." [PSI:PI] +is_a: MS:1001055 ! modification parameters +is_a: MS:1003026 ! named element in mzIdentML + +[Term] +id: MS:1003022 +name: Variable modification +def: "Post-translational modification which may or may not be present at a residue type." [PSI:PI] +is_a: MS:1001055 ! modification parameters +is_a: MS:1003026 ! named element in mzIdentML + +[Term] +id: MS:1003023 +name: OpenPepXL +def: "Cross-Linking MS search engine." [PSI:PI] +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1003024 +name: OpenPepXL:score +def: "The OpenPepXL score for a crosslink spectrum match." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +is_a: MS:1001153 ! search engine specific score +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003025 +name: named element +def: "A named element that is an attribute in a proteomics standards file." [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1003026 +name: named element in mzIdentML +def: "A named element that is an attribute in a mzIdentML file." [PSI:PI] +is_a: MS:1003025 ! named element + +[Term] +id: MS:1003027 +name: named element in mzML +def: "A named element that is an attribute in a mzML file." [PSI:PI] +is_a: MS:1003025 ! named element + +[Term] +id: MS:1003028 +name: Orbitrap Exploris 480 +def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003029 +name: Orbitrap Eclipse +def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003030 +name: Mascot:MinNumSigUniqueSeqs +def: "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI] +is_a: MS:1002095 ! Mascot input parameter +relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1003031 +name: CPTAC accession number +def: "Main identifier of a CPTAC dataset." [PSI:PI] +is_a: MS:1000878 ! external reference identifier +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003032 +name: compound identification confidence code in MS-DIAL +def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] +is_a: MS:1002895 ! small molecule identification attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003033 +name: molecular entity attribute +def: "Non-inherent characteristic attributed to a molecular entity." [PSI:PI] +relationship: part_of MS:1000881 ! molecular entity + +[Term] +id: MS:1003034 +name: atom +def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] +is_a: MS:1000881 ! molecular entity + +[Term] +id: MS:1003035 +name: small molecule +def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003036 +name: metabolite +def: "Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003037 +name: ribonucleotide +def: "Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003038 +name: deoxyribonucleotide +def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003039 +name: amino acid +def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003040 +name: monosaccharide +def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide] +is_a: MS:1003035 ! small molecule + +[Term] +id: MS:1003041 +name: nucleic acid +def: "Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003042 +name: polysaccharide +def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003043 +name: number of residues +def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] +is_a: MS:1000887 ! peptide attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003044 +name: number of missed cleavages +def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] +is_a: MS:1000887 ! peptide attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003045 +name: peptide-to-protein mapping +def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] +is_a: MS:1000887 ! peptide attribute + +[Term] +id: MS:1003046 +name: peptide-to-protein mapping attribute +def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] +is_a: MS:1003045 ! peptide-to-protein mapping + +[Term] +id: MS:1003047 +name: protein sequence offset +def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003048 +name: number of enzymatic termini +def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] +is_a: MS:1003046 ! peptide-to-protein mapping attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003049 +name: peptidoform +def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] +is_a: MS:1000860 ! peptide + +[Term] +id: MS:1003050 +name: peptidoform attribute +def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI] +relationship: part_of MS:1003049 ! peptidoform + +[Term] +id: MS:1003051 +name: peptidoform ion +def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] +is_a: MS:1003049 ! peptidoform +synonym: "precursor" RELATED [] +synonym: "precursor ion" RELATED [] +synonym: "parent ion" RELATED [] + +[Term] +id: MS:1003052 +name: peptidoform ion property +def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI] +relationship: part_of MS:1003051 ! peptidoform ion + +[Term] +id: MS:1003053 +name: theoretical monoisotopic m/z +def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] +is_a: MS:1003052 ! peptidoform ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003054 +name: theoretical average m/z +def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] +is_a: MS:1003052 ! peptidoform ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003055 +name: adduct +def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct] +is_a: MS:1000859 ! molecule + +[Term] +id: MS:1003056 +name: adduct ion property +def: "Physical measurable characteristic of an adduct ion." [PSI:PI] +relationship: part_of MS:1000353 ! adduct ion + +[Term] +id: MS:1003057 +name: scan number +def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] +is_a: MS:1000503 ! scan attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003058 +name: spectrum property +def: "Inherent or measurable characteristic of a spectrum." [PSI:PI] +relationship: part_of MS:1000442 ! spectrum + +[Term] +id: MS:1003059 +name: number of peaks +def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003060 +name: number of data points +def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] +is_a: MS:1003058 ! spectrum property +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003061 +name: library spectrum name +def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term +synonym: "spectrum name" EXACT [] + +[Term] +id: MS:1003062 +name: library spectrum index +def: "Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0." [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003063 +name: universal spectrum identifier +def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term +synonym: "USI" EXACT [] + +[Term] +id: MS:1003064 +name: spectrum aggregation attribute +def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute + +[Term] +id: MS:1003065 +name: spectrum aggregation type +def: "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute + +[Term] +id: MS:1003066 +name: singleton spectrum +def: "Spectrum that is not the result of some aggregation process." [PSI:PI] +is_a: MS:1003065 ! spectrum aggregation type + +[Term] +id: MS:1003067 +name: consensus spectrum +def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] +is_a: MS:1003065 ! spectrum aggregation type + +[Term] +id: MS:1003068 +name: best replicate spectrum +def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] +is_a: MS:1003065 ! spectrum aggregation type + +[Term] +id: MS:1003069 +name: number of replicate spectra available +def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003070 +name: number of replicate spectra used +def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003071 +name: spectrum origin attribute +def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] +is_a: MS:1000499 ! spectrum attribute + +[Term] +id: MS:1003072 +name: spectrum origin type +def: "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI] +is_a: MS:1003071 ! spectrum origin attribute + +[Term] +id: MS:1003073 +name: observed spectrum +def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003074 +name: predicted spectrum +def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003075 +name: demultiplexed spectrum +def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003076 +name: uninterpreted spectrum +def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] +is_a: MS:1000442 ! spectrum + +[Term] +id: MS:1003077 +name: interpreted spectrum +def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] +is_a: MS:1000442 ! spectrum + +[Term] +id: MS:1003078 +name: interpreted spectrum attribute +def: "Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI] +relationship: part_of MS:1003077 ! interpreted spectrum + +[Term] +id: MS:1003079 +name: total unassigned intensity fraction +def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003080 +name: top 20 peak unassigned intensity fraction +def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003081 +name: unidentified modification monoisotopic mass delta +def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_units UO:0000221 ! dalton +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003082 +name: MS-DIAL +def: "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372] +is_a: MS:1002878 ! small molecule analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003083 +name: raw data file +def: "Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file)." [PSI:MS] +is_a: MS:1000577 ! source data file + +[Term] +id: MS:1003084 +name: processed data file +def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS] +is_a: MS:1000577 ! source data file +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003085 +name: previous MSn-1 scan precursor intensity +def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS] +is_a: MS:1001141 ! intensity of precursor ion +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003086 +name: precursor apex intensity +def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS] +is_a: MS:1001141 ! intensity of precursor ion +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003087 +name: supported by repository but incomplete data and/or metadata +def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available." [PSI:PI] +is_a: MS:1002844 ! Experiment additional parameter + +[Term] +id: MS:1003088 +name: truncation and zlib compression +def: "Data array compression using mantissa bit truncation followed by zlib compression." [https://github.com/biospi/pwiz] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1003089 +name: truncation, delta prediction and zlib compression +def: "Data array compression using mantissa bit truncation, delta prediction and zlib compression." [https://github.com/biospi/pwiz] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1003090 +name: truncation, linear prediction and zlib compression +def: "Data array compression using mantissa bit truncation, linear prediction and zlib compression." [https://github.com/biospi/pwiz] +is_a: MS:1000572 ! binary data compression type + +[Term] +id: MS:1003091 +name: binary data compression parameter +def: "Settable parameter for a binary data compression event." [PSI:MS] +relationship: part_of MS:1000442 ! spectrum +relationship: part_of MS:1000625 ! chromatogram + +[Term] +id: MS:1003092 +name: number of mantissa bits truncated +def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS] +is_a: MS:1003091 ! binary data compression parameter +relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term + +[Term] +id: MS:1003093 +name: Lys-N +def: "Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues." [https://en.wikipedia.org/wiki/Lys-N] +is_a: MS:1001045 ! cleavage agent name +relationship: has_regexp MS:1001335 ! (?=K) + +[Term] +id: MS:1003094 +name: Orbitrap Exploris 240 +def: "Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003095 +name: Orbitrap Exploris 120 +def: "Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003096 +name: LTQ Orbitrap Velos Pro +def: "Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003097 +name: MaxQuant protein group-level score +def: "The probability based MaxQuant protein group score." [PSI:MS] +is_a: MS:1002368 ! search engine specific score for protein groups +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003098 +name: Andromeda peptide PEP +def: "Peptide probability from Andromeda." [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003099 +name: MaxQuant-DIA peptide PEP +def: "Peptide probability from MaxQuant-DIA algorithm." [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003100 +name: MaxQuant-DIA score +def: "PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003101 +name: MaxQuant-DIA PEP +def: "PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003102 +name: NIST msp comment +def: "Term for a comment field withing the NIST msp file format" [PSI:MS] +is_a: MS:1000499 ! spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003103 +name: ion annotation format +def: "Annotation format used for annotating individual spectrum ion peaks." [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute + +[Term] +id: MS:1003104 +name: mzPAF peptide ion annotation format +def: "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS] +is_a: MS:1003103 ! ion annotation format +synonym: "peptide ion annotation format" EXACT [] + +[Term] +id: MS:1003105 +name: crosslinked peptide ion annotation format +def: "Annotation format designed specifically for crosslinked peptide ion peaks." [PSI:MS] +synonym: "cross-linked peptide ion annotation format" EXACT [] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003106 +name: glycan ion annotation format +def: "Annotation format designed specifically for glycan ion peaks." [PSI:MS] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003107 +name: lipid ion annotation format +def: "Annotation format designed specifically for lipid ion peaks." [PSI:MS] +is_a: MS:1003103 ! ion annotation format + +[Term] +id: MS:1003108 +name: PatternLab +def: "PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003109 +name: SIM-XL +def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003110 +name: SIM-XL score +def: "SIM-XL identification search engine score" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003111 +name: QUIN-XL +def: "Quantification of crosslinked peptides in complex protein mixtures" [PSI:MS] +is_a: MS:1001139 ! quantitation software name + +[Term] +id: MS:1003112 +name: Orbitrap ID-X +def: "Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003113 +name: OpenMS:ConsensusID PEP +def: "The OpenMS ConsesusID tool posterior error probability" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003114 +name: OpenMS:Best PSM Score +def: "The score of the best PSM selected by the underlying identification tool" [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003115 +name: OpenMS:Target-decoy PSM q-value +def: "The OpenMS Target-decoy q-values at PSM level" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003116 +name: OpenMS:Target-decoy peptide q-value +def: "The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS] +is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003117 +name: OpenMS:Target-decoy protein q-value +def: "The OpenMS Target-decoy q-values at protein level" [PSI:MS] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003118 +name: EPIFANY +def: "A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework" [PSI:MS] +is_a: MS:1001456 ! analysis software +is_a: MS:1000752 ! TOPP software + +[Term] +id: MS:1003119 +name: EPIFANY:Protein posterior probability +def: "Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS] +is_a: MS:1002363 ! search engine specific score for proteins +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003120 +name: OpenMS:LFQ intensity +def: "The data type LFQ intensity produced by OpenMS." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003121 +name: OpenMS:LFQ spectral count +def: "The data type LFQ spectral count produced by OpenMS." [PSI:MS] +is_a: MS:1001805 ! quantification datatype +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003122 +name: rapifleX +def: "Bruker Daltonics' rapiflex: MALDI TOF/TOF." [PSI:MS] +is_a: MS:1001534 ! Bruker Daltonics flex series + +[Term] +id: MS:1003123 +name: Bruker Daltonics timsTOF series +def: "Bruker Daltonics timsTOF series" [PSI:MS] +is_a: MS:1000122 ! Bruker Daltonics instrument model + +[Term] +id: MS:1003124 +name: timsTOF fleX +def: "Bruker Daltonics' timsTOF fleX" [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003125 +name: ProSight:spectral Q-value +def: "ProSight spectrum-level Q-value." [PSI:MS] +is_a: MS:1002354 ! PSM-level q-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003126 +name: ProSight:spectral P-score +def: "ProSight spectrum-level P-score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003127 +name: ProSight:spectral E-value +def: "ProSight spectrum-level E-value." [PSI:MS] +is_a: MS:1002353 ! PSM-level e-value +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003128 +name: ProSight:spectral C-score +def: "ProSight spectrum-level C-score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003129 +name: proteoform-level Q-value +def: "Estimation of the Q-value for proteoforms." [PSI:MS] +is_a: MS:1002905 ! proteoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003130 +name: ProSight:proteoform Q-value +def: "ProSight proteoform-level Q-value." [PSI:MS] +is_a: MS:1003129 ! proteoform-level Q-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003131 +name: isoform-level identification attribute +def: "Isoform level information." [PSI:MS] +is_a: MS:1002694 ! single identification result attribute + +[Term] +id: MS:1003132 +name: isoform-level identification statistic +def: "Identification confidence metric for a isoform." [PSI:MS] +is_a: MS:1003131 ! isoform-level identification attribute + +[Term] +id: MS:1003133 +name: isoform-level Q-value +def: "Estimation of the Q-value for isoforms." [PSI:MS] +is_a: MS:1003132 ! isoform-level identification statistic +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003134 +name: ProSight:isoform Q-value +def: "ProSight isoform-level Q-value." [PSI:MS] +is_a: MS:1003133 ! isoform-level Q-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003135 +name: ProSight:protein Q-value +def: "ProSight protein-level Q-value." [PSI:MS] +is_a: MS:1001869 ! protein-level q-value +relationship: has_order MS:1002109 ! lower score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003136 +name: ProSight input parameter +def: "Search engine input parameters specific to ProSight." [PSI:MS] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1003137 +name: TDPortal input parameter +def: "Search engine input parameters specific to TDPortal." [PSI:MS] +is_a: MS:1001302 ! search engine specific input parameter + +[Term] +id: MS:1003138 +name: ProSight:Run delta m mode +def: "If true, runs delta m mode in ProSight." [PSI:MS] +is_a: MS:1003136 ! ProSight input parameter +is_a: MS:1003137 ! TDPortal input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003139 +name: ProSight:Run Subsequence Search mode +def: "If true, runs Subsequence Search mode in ProSight." [PSI:MS] +is_a: MS:1003136 ! ProSight input parameter +is_a: MS:1003137 ! TDPortal input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003140 +name: ProSight:Run Annotated Proteoform Search mode +def: "If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS] +is_a: MS:1003136 ! ProSight input parameter +is_a: MS:1003137 ! TDPortal input parameter +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003141 +name: ProSight +def: "ProSight: Database search engine for top-down proteomics." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003142 +name: TDPortal +def: "TDPortal: Database search engine for top-down proteomics." [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003143 +name: mass array +def: "A data array of mass values." [PSI:MS] +xref: binary-data-type:MS\:1000521 "32-bit float" +xref: binary-data-type:MS\:1000523 "64-bit float" +is_a: MS:1000513 ! binary data array +relationship: has_units UO:0000221 ! dalton + +[Term] +id: MS:1003144 +name: Triple Quad 7500 +def: "SCIEX Triple Quad 7500." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1003145 +name: ThermoRawFileParser +def: "Cross-platform software to convert Thermo RAW files to a number of open formats." [DOI:10.1021/acs.jproteome.9b00328, PMID:31755270] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003146 +name: pyteomics +def: "Python module that helps handling various proteomics data analysis tasks." [DOI:10.1021/acs.jproteome.8b00717, PMID:30576148] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003147 +name: PTMProphet probability +def: "Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003148 +name: PTMProphet mean best probability +def: "PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003149 +name: PTMProphet normalized information content +def: " PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003150 +name: PTMProphet information content +def: " PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003151 +name: SHA-256 +def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS] +is_a: MS:1000561 ! data file checksum type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003152 +name: GCMS-QP2010SE +def: "Shimadzu Scientific Instruments GCMS-QP2010SE." [PSI:MS] +is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model + +[Term] +id: MS:1003153 +name: raw ion mobility drift time array +def: "Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003154 +name: deconvoluted ion mobility array +def: "Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003155 +name: deconvoluted inverse reduced ion mobility array +def: "Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units MS:1002814 ! volt-second per square centimeter +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003156 +name: deconvoluted ion mobility drift time array +def: "Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] +is_a: MS:1002893 ! ion mobility array +relationship: has_units UO:0000028 ! millisecond +relationship: has_units UO:0000010 ! second +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003157 +name: scanning quadrupole position lower bound m/z array +def: "Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003158 +name: scanning quadrupole position upper bound m/z array +def: "Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] +is_a: MS:1000513 ! binary data array +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003159 +name: isolation window full range +def: "Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range." [PSI:MS] +is_a: MS:1000792 ! isolation window attribute + +[Term] +id: MS:1003160 +name: mzQC format +def: "Proteomics Standards Initiative mzQC format for quality control data." [PSI:MS] +is_a: MS:1003161 ! quality control data format + +[Term] +id: MS:1003161 +name: quality control data format +def: "Grouping term for quality control data formats." [PSI:MS] +is_a: MS:1001459 ! file format + +[Term] +id: MS:1003162 +name: PTX-QC +def: "Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization." [DOI:10.1021/acs.jproteome.5b00780, PMID:26653327, https://github.com/cbielow/PTXQC/] +is_a: MS:1001456 ! analysis software +synonym: "PTXQC" EXACT [] + +[Term] +id: MS:1003163 +name: analyte mixture members +def: "The set of analyte identifiers that compose an interpretation of a spectrum." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type MS:1002712 ! list of integers + +[Term] +id: MS:1003164 +name: QuaMeter IDFree +def: "QuaMeter IDFree software for QC metric calculation." [DOI:10.1021/ac4034455, PMID:24494671] +is_a: MS:1001456 ! analysis software +synonym: "QuaMeter" EXACT [] + +[Term] +id: MS:1003165 +name: iMonDB +def: "iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files." [DOI:10.1021/acs.jproteome.5b00127, PMID:25798920, https://github.com/bittremieux/iMonDB] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003166 +name: assigned intensity fraction +def: "Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum" [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003167 +name: MSn-1 isolation window precursor purity +def: "The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte" [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003168 +name: library spectrum comment +def: "A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools." [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003169 +name: proforma peptidoform sequence +def: "Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation" [PSI:PI] +is_a: MS:1000889 ! peptidoform sequence +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003170 +name: spectral library +def: "A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments" [PSI:PI] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1003171 +name: spectral library attribute +def: "An attribute of a spectral library" [PSI:PI] +relationship: part_of MS:1003170 ! spectral library + +[Term] +id: MS:1003172 +name: library spectrum +def: "An entry in a spectral library representing a spectrum" [PSI:PI] +relationship: part_of MS:1003170 ! spectral library + +[Term] +id: MS:1003173 +name: numeric attribute +def: "An attribute that takes on a numeric value" [PSI:PI] +is_a: MS:1000547 ! object attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003174 +name: attribute maximum +def: "The maximum value for this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003175 +name: attribute minimum +def: "The minimum value for this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003176 +name: attribute mean +def: "The arithmetic mean value for this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003177 +name: attribute standard deviation +def: "The standard deviation (exact value of population, or estimate from sample) of this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003178 +name: attribute coefficient of variation +def: "The coefficient of variation of this attribute, i.e. standard deviation divided by the mean" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003179 +name: attribute summary value +def: "The most appropriate summary value of the attribute, usually but not necessarily the mean" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003180 +name: attribute median +def: "The median of this attribute" [PSI:PI] +relationship: part_of MS:1003171 ! numeric attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003181 +name: combined dissociation method +def: "Combination of two or more dissociation methods that are known by a special term." [PSI:PI] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1003182 +name: electron-transfer/collision-induced dissociation +def: "Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID)." [PSI:PI] +synonym: "ETciD" EXACT [] +is_a: MS:1003181 ! combined dissociation method + +[Term] +id: MS:1003183 +name: Synapt XS +def: "Waters oa-ToF based Synapt XS." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003184 +name: SELECT SERIES Cyclic IMS +def: "Waters oa-ToF based SELECT SERIES Cyclic IMS." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003185 +name: SELECT SERIES MRT +def: "Waters oa-ToF based SELECT SERIES MRT." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003186 +name: library format version +def: "Version number of the [PSI] library format specification" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003187 +name: library identifier +def: "Short identifier for the library for easy reference, preferably but not necessarily globally unique" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003188 +name: library name +def: "A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library." [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003189 +name: library description +def: "Extended free-text description of the library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003190 +name: library version +def: "Version number of the library, usually refering to a certain release of a continually updated library " [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003191 +name: library URI +def: "URI or URL that uniquely identifies the library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003192 +name: decoy spectrum +def: "A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching" [PSI:PI] +is_a: MS:1003072 ! spectrum origin type + +[Term] +id: MS:1003193 +name: shuffle-and-reposition decoy spectrum +def: "A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence." [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003194 +name: precursor shift decoy spectrum +def: "A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum." [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003195 +name: unnatural peptidoform decoy spectrum +def: "A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform" [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003196 +name: unrelated species decoy spectrum +def: "A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample" [PSI:PI] +is_a: MS:1003192 ! decoy spectrum + +[Term] +id: MS:1003197 +name: license URI +def: "URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/)" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003198 +name: copyright notice +def: "Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003199 +name: change log +def: "Extended free-text description of the difference from the previous version" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003200 +name: software version +def: "Version number of the software package used for library creation" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003201 +name: library provenance attribute +def: "Abstract term containing several different types of provenance information" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003202 +name: BiblioSpec +def: "A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington" [PSI:PI] +is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software + +[Term] +id: MS:1003203 +name: constituent spectrum file +def: "Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible." [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003204 +name: constituent identification file +def: "Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible" [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003205 +name: constituent library file +def: "Source library URI which(at least) a subset of spectra were extracted from." [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003206 +name: library creation log +def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n" [PSI:PI] +is_a: MS:1003201 ! library provenance attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003207 +name: library creation software +def: "Library creation software" [PSI:MS] +is_a: MS:1000531 ! software +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003208 +name: experimental precursor monoisotopic m/z +def: "The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum." [PSI:MS] +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1003295 ! summary statistics of replicates +relationship: has_units MS:1000040 ! m/z +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003209 +name: monoisotopic m/z deviation +def: "The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum." [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute +is_a: MS:1003295 ! summary statistics of replicates +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003210 +name: average m/z deviation +def: "The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum." [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute +is_a: MS:1003295 ! summary statistics of replicates +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003211 +name: library spectrum attribute set +def: "A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003212 +name: library attribute set name +def: "A name to refer to a library attribute set" [PSI:PI] +relationship: part_of MS:1003211 ! library spectrum attribute set +relationship: part_of MS:1003238 ! library analyte attribute set +relationship: part_of MS:1003239 ! library interpretation attribute set +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003213 +name: mass spectrometry acquisition method +def: "Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS] +is_a: MS:1000524 ! data file content +is_a: MS:1001954 ! acquisition parameter +relationship: part_of MS:1003350 ! mass spectrometry proteomics + +[Term] +id: MS:1003214 +name: mass spectrometry acquisition method aspect +def: "Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS] +is_a: MS:1001458 ! spectrum generation information +relationship: part_of MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003215 +name: data-independent acquisition +def: "Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions." [PSI:MS] +synonym: "DIA" EXACT [] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003216 +name: dissociation of full mass range +def: "Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003217 +name: dissociation of scanning quadrupole across a specified mass range +def: "Mass spectrometer data acquisition method wherein ????." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003218 +name: dissociation of sequential mass ranges +def: "Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003219 +name: ion mobility separation +def: "Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect + +[Term] +id: MS:1003220 +name: adduct deconvolution +def: "Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003221 +name: data-dependent acquisition +def: "Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run." [PSI:MS] +is_a: MS:1003214 ! mass spectrometry acquisition method aspect +is_a: MS:1003213 ! mass spectrometry acquisition method +synonym: "DDA" EXACT [] + +[Term] +id: MS:1003222 +name: ion mobility deconvolution +def: "Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003224 +name: data independent acquisition from dissociation of sequential mass ranges +def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC." [PSI:MS] +is_a: MS:1003218 ! dissociation of sequential mass ranges +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003225 +name: data independent acquisition from dissociation of sequential mass ranges after ion mobility separation +def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF." [PSI:MS] +is_a: MS:1003218 ! dissociation of sequential mass ranges +is_a: MS:1003219 ! ion mobility separation +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003226 +name: data independent acquisition from dissociation of full mass range after ion mobility separation +def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF." [PSI:MS] +is_a: MS:1003216 ! dissociation of full mass range +is_a: MS:1003219 ! ion mobility separation +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003227 +name: data independent acquisition from dissociation of full mass range +def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID." [PSI:MS] +is_a: MS:1003216 ! dissociation of full mass range +is_a: MS:1003219 ! ion mobility separation +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003228 +name: data independent acquisition from dissociation of scanning quadrupole across mass range +def: "Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR." [PSI:MS] +is_a: MS:1003215 ! data-independent acquisition +is_a: MS:1003217 ! dissociation of scanning quadrupole across a specified mass range +is_a: MS:1003213 ! mass spectrometry acquisition method + +[Term] +id: MS:1003229 +name: timsTOF +def: "Bruker Daltonics' timsTOF." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003230 +name: timsTOF Pro 2 +def: "Bruker Daltonics' timsTOF Pro 2." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003231 +name: timsTOF SCP +def: "Bruker Daltonics' timsTOF SCP." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003232 +name: PeakForest +def: "comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB)." [https://peakforest.org/] +is_a: MS:1001456 ! analysis software +is_a: MS:1003207 ! library creation software +is_a: MS:1002878 ! small molecule analysis software + +[Term] +id: MS:1003234 +name: library spectrum attribute +def: "An attribute that describes information about an entry in a spectral library" [PSI:PI] +relationship: part_of MS:1003172 ! library spectrum + +[Term] +id: MS:1003235 +name: paper spray ionization +def: "The ionization of analytes from a piece of paper by applying a solvent and voltage." [PSI:MS] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1003237 +name: library spectrum key +def: "An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library." [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003238 +name: library analyte attribute set +def: "A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003239 +name: library interpretation attribute set +def: "A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] +is_a: MS:1003171 ! spectral library attribute + +[Term] +id: MS:1003240 +name: peak intensity transform +def: "A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores" [PSI:PI] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003241 +name: square root transform +def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots" [PSI:PI] +is_a: MS:1003240 ! peak intensity transform + +[Term] +id: MS:1003242 +name: rank transform +def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks" [PSI:PI] +is_a: MS:1003240 ! peak intensity transform + +[Term] +id: MS:1003243 +name: adduct ion mass +def: "The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton)" [PSI:PI] +is_a: MS:1003056 ! adduct ion property +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003244 +name: peptide accession number +def: "Accession number (e.g. in PeptideAtlas) of the peptide sequence" [PSI:PI] +is_a: MS:1003050 ! peptidoform attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003245 +name: Q Exactive UHMR +def: "Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003246 +name: ultraviolet photodissociation +def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons." [PSI:MS] +synonym: "UVPD" EXACT [] +is_a: MS:1000435 ! photodissociation + +[Term] +id: MS:1003247 +name: negative electron transfer dissociation +def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation." [DOI:10.1016/j.jasms.2005.01.015, PSI:MS] +synonym: "NETD" EXACT [] +is_a: MS:1000044 ! dissociation method + +[Term] +id: MS:1003248 +name: proton transfer reaction +def: "Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation." [DOI:10.1002/mas.20048, PSI:MS] +synonym: "PTR" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1003249 +name: proton transfer charge reduction +def: "Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte." [PSI:MS] +synonym: "PTCR" EXACT [] +is_a: MS:1000008 ! ionization type + +[Term] +id: MS:1003250 +name: count of identified peptidoforms +def: "The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] +is_a: MS:1002702 ! peptide sequence-level result list attribute +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1003251 +name: count of identified spectra +def: "The number of spectra that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] +is_a: MS:1002700 ! PSM-level result list attribute +is_a: MS:4000003 ! single value +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_metric_category MS:4000008 ! ID based metric + +[Term] +id: MS:1003252 +name: Xevo G2-XS QTof +def: "Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer." [PSI:PI] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003253 +name: DIA-NN +def: "A universal software for data-independent acquisition (DIA) proteomics data processing" [PMID:31768060, https://github.com/vdemichev/DiaNN] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003254 +name: peak attribute +def: "An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. " [PSI:PI] +relationship: part_of MS:1000231 ! peak + +[Term] +id: MS:1003255 +name: pre-decharged charge state +def: "For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. " [PSI:PI] +is_a: MS:1003254 ! peak attribute + +[Term] +id: MS:1003256 +name: peptidoform ion attribute +def: "Non-inherent characteristic attributed to a peptidoform" [PSI:PI] +relationship: part_of MS:1003051 ! peptidoform ion + +[Term] +id: MS:1003257 +name: library spectrum cross reference +def: "A link from one spectrum to another spectrum of interest " [PSI:PI] +is_a: MS:1003234 ! library spectrum attribute + +[Term] +id: MS:1003258 +name: related spectrum +def: "A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. " [PSI:PI] +is_a: MS:1003257 ! library spectrum cross reference + +[Term] +id: MS:1003259 +name: related spectrum keys +def: "A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. " [PSI:PI] +is_a: MS:1003258 ! related spectrum +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003260 +name: related spectrum USI +def: "A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] +is_a: MS:1003258 ! related spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003261 +name: related spectrum description +def: "A free-text string describing the related spectrum and/or its relationship to this spectrum" [PSI:PI] +relationship: part_of MS:1003258 ! related spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003262 +name: similar spectrum +def: "A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion." [PSI:PI] +is_a: MS:1003257 ! library spectrum cross reference + +[Term] +id: MS:1003263 +name: similar spectrum keys +def: "A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. " [PSI:PI] +is_a: MS:1003262 ! similar spectrum +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003264 +name: similar spectrum USI +def: "A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] +is_a: MS:1003262 ! similar spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003265 +name: spectrum cluster +def: "A group of spectra that are spectrally similar to each other" [PSI:PI] +relationship: part_of MS:1003170 ! spectral library + +[Term] +id: MS:1003266 +name: spectrum cluster attribute +def: "A non-inherent characteristic of a spectrum cluster" [PSI:PI] +relationship: part_of MS:1003265 ! spectrum cluster + +[Term] +id: MS:1003267 +name: spectrum cluster key +def: "An ordinal number uniquely identifying a spectrum cluster. It should start with 1." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003268 +name: spectrum cluster member spectrum keys +def: "A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003269 +name: spectrum cluster member USI +def: "A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003270 +name: proforma peptidoform ion notation +def: "A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type." [PSI:PI] +is_a: MS:1003256 ! peptidoform ion attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003271 +name: peak annotation +def: "The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum." [PSI:PI] +relationship: part_of MS:1000231 ! peak + +[Term] +id: MS:1003272 +name: peak annotation string +def: "A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'." [PSI:PI] +relationship: part_of MS:1003271 ! peak annotation +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003273 +name: peak annotation confidence +def: "A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'." [PSI:PI] +relationship: part_of MS:1003271 ! peak annotation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003274 +name: peak annotation confidence metric +def: "A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1." [PSI:PI] +is_a: MS:1003078 ! interpreted spectrum attribute + +[Term] +id: MS:1003275 +name: other attribute name +def: "A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value" [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003276 +name: other attribute value +def: "A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name" [PSI:MS] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_type MS:1002711 ! The allowed value-type for this CV term +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term +relationship: has_value_type MS:1002713 ! The allowed value-type for this CV term + +[Term] +id: MS:1003277 +name: value between -1 and 1 inclusive +def: "Value range for signed normalized score values." [PSI:PI] +is_a: MS:1002304 ! domain range + +[Term] +id: MS:1003278 +name: m/z variability of peak +def: "A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003254 ! peak attribute + +[Term] +id: MS:1003279 +name: observation frequency of peak +def: "The frequency at which this peak is observed among replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003254 ! peak attribute +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003280 +name: intensity variability of peak +def: "A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003254 ! peak attribute + +[Term] +id: MS:1003281 +name: Casanovo +def: "Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/." [https://github.com/Noble-Lab/casanovo/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003282 +name: Bruker TSF format +def: "Bruker TSF raw file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003283 +name: Bruker TSF nativeID format +def: "Native format defined by frame=xsd:nonNegativeInteger." [PSI:MS] +is_a: MS:1000767 ! native spectrum identifier format + +[Term] +id: MS:1003284 +name: Bruker TSF nativeID format, combined spectra +def: "Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] +is_a: MS:1002646 ! native spectrum identifier format, combined spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + + +[Term] +id: MS:1003285 +name: standard deviation of m/z values of peak among replicates +def: "The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003278 ! m/z variability of peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003286 +name: coefficient of variation of intensity of peak among replicates +def: "The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003280 ! intensity variability of peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003287 +name: standard deviation of intensity of peak among replicates +def: "The standard deviation of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI] +is_a: MS:1003280 ! intensity variability of peak +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003288 +name: number of unassigned peaks +def: "The number of unassigned peaks in the spectrum." [NIST] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003289 +name: intensity of highest unassigned peak +def: "The intensity of the highest unassigned peak in the spectrum." [NIST] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003290 +name: number of unassigned peaks among top 20 peaks +def: "The number of unassigned peaks among the most intense 20 peaks in the spectrum." [NIST] +is_a: MS:1003078 ! interpreted spectrum attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003291 +name: Luciphor deltaScore +def: "Luciphor phosphosite localization score" [PSI:MS] +is_a: MS:1001968 ! PTM localization PSM-level statistic +relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring + +[Term] +id: MS:1003292 +name: TSQ Altis Plus +def: "Thermo Scientific TSQ Altis Plus Triple Quadrupole MS." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003293 +name: ZenoTOF 7600 +def: "SCIEX ZenoTOF 7600." [PSI:MS] +is_a: MS:1000121 ! SCIEX instrument model + +[Term] +id: MS:1003294 +name: electron activated dissociation +def: "A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins." [PSI:MS] +synonym: "EAD" EXACT [] +is_a: MS:1000250 ! electron capture dissociation + +[Term] +id: MS:1003295 +name: summary statistics of replicates +def: "Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum." [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute + +[Term] +id: MS:1003296 +name: number of replicates spectra used from source +def: "The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name'" [PSI:PI] +is_a: MS:1003064 ! spectrum aggregation attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003297 +name: contributing replicate spectrum +def: "A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum." [PSI:PI] +is_a: MS:1003257 ! library spectrum cross reference + +[Term] +id: MS:1003298 +name: contributing replicate spectrum keys +def: "A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys." [PSI:PI] +relationship: part_of MS:1003297 ! contributing replicate spectrum +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term + +[Term] +id: MS:1003299 +name: contributing replicate spectrum USI +def: "A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers." [PSI:PI] +relationship: part_of MS:1003297 ! contributing replicate spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003300 +name: spectrum match +def: "Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte." [PSI:PI] +relationship: part_of MS:1001000 ! spectrum interpretation + +[Term] +id: MS:1003301 +name: peptide-spectrum match +def: "Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence." [PSI:PI] +is_a: MS:1003300 ! spectrum match +synonym: "PSM" EXACT [] + +[Term] +id: MS:1003302 +name: spectrum-spectrum match +def: "Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering." [PSI:PI] +is_a: MS:1003300 ! spectrum match +synonym: "SSM" EXACT [] + +[Term] +id: MS:1003303 +name: spectral similarity +def: "A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone." [PSI:PI] +is_a: MS:1002694 ! single identification result attribute +relationship: part_of MS:1003302 ! spectrum-spectrum match + +[Term] +id: MS:1003304 +name: spectral dot product +def: "The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity." [PSI:PI] +is_a: MS:1003303 ! spectral similarity +synonym: "cosine similarity" EXACT [] +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003305 +name: spectral Euclidean distance +def: "The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space." [PSI:PI] +is_a: MS:1003303 ! spectral similarity +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003306 +name: shared peak count +def: "The number of peaks with closely matching m/z values that are common to two spectra." [PSI:PI] +is_a: MS:1003303 ! spectral similarity +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:1003307 +name: normalized spectral angle +def: "The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi." [https://doi.org/10.1074/mcp.O113.036475] +is_a: MS:1003303 ! spectral similarity +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003308 +name: spectral Pearson correlation +def: "The Pearson's rho statistic between a pair of points representing two vectorized spectra." [PSI:PI] +is_a: MS:1003303 ! spectral similarity +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + + +[Term] +id: MS:1003309 +name: Goslin +def: "The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature." [PMID:32589019, https://github.com/lifs-tools/goslin] +is_a: MS:1001457 ! data processing software +is_a: MS:1002414 ! postprocessing software +is_a: MS:1002964 ! lipidomics analysis software + +[Term] +id: MS:1003310 +name: Lipid shorthand identification confidence level +def: "Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'." [PMID:33037133] +is_a: MS:1002895 ! small molecule identification attribute + +[Term] +id: MS:1003311 +name: Lipid empirical score +def: "The lipid empirical score is a point-based lipid class-specific scoring system based on MS and other evidence sources as defined by the Lipidomics Standards Initiative (LSI). The score has a numeric value between 0 and 100. Score values are lipid class-specific and are therefore not immediately comparable between lipid classes." [] +is_a: MS:1002888 ! small molecule confidence measure +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003312 +name: Lipid shorthand identification confidence - Category +def: "Lipid shorthand identification confidence level 'Category'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003313 +name: Lipid shorthand identification confidence - Class +def: "Lipid shorthand identification confidence level 'Class'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003314 +name: Lipid shorthand identification confidence - Species +def: "Lipid shorthand identification confidence level 'Species'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003315 +name: Lipid shorthand identification confidence - Phosphate-position +def: "Lipid shorthand identification confidence level 'Phosphate-position'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003316 +name: Lipid shorthand identification confidence - Molecular species +def: "Lipid shorthand identification confidence level 'Molecular species'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003317 +name: Lipid shorthand identification confidence - sn-position +def: "Lipid shorthand identification confidence level 'sn-position'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003318 +name: Lipid shorthand identification confidence - DBE pos +def: "Lipid shorthand identification confidence level 'DBE pos'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003319 +name: Lipid shorthand identification confidence - Structure defined +def: "Lipid shorthand identification confidence level 'Structure defined'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003320 +name: spectrum cluster size +def: "The number of spectra in a spectrum cluster." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:integer + +[Term] +id: MS:1003321 +name: summary statistics of clustered spectra +def: "Summary statistics of an attribute among all spectra of a spectrum cluster." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute + +[Term] +id: MS:1003322 +name: spectrum cluster best representative +def: "Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:string + +[Term] +id: MS:1003323 +name: spectrum cluster consensus spectrum +def: "Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not." [PSI:PI] +is_a: MS:1003266 ! spectrum cluster attribute +relationship: has_value_type xsd:string + +[Term] +id: MS:1003324 +name: spectral dot product to aggregated spectrum +def: "Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum." [PSI:PI] +is_a: MS:1003295 ! summary statistics of replicates +is_a: MS:1003304 ! spectral dot product +relationship: has_value_type xsd:float + +[Term] +id: MS:1003325 +name: Lipid shorthand identification confidence - Full structure +def: "Lipid shorthand identification confidence level 'Full structure'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003326 +name: Lipid shorthand identification confidence - Complete structure +def: "Lipid shorthand identification confidence level 'Complete structure'." [PMID:33037133] +is_a: MS:1003310 ! Lipid shorthand identification confidence level + +[Term] +id: MS:1003327 +name: number of identified protein groups +def: "The number of protein groups that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] +is_a: MS:1002405 ! protein group-level result list attribute +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:1003328 +name: number of identified proteoforms +def: "The number of proteoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] +is_a: MS:1001085 ! protein-level identification attribute +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:1003329 +name: looplink spectrum identification item +def: "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink." [PSI:MS] +synonym: "loop-link spectrum identification item" EXACT [] +is_a: MS:1002508 ! crosslinking attribute + +[Term] +id: MS:1003330 +name: noncovalently associated peptides search +def: "Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions." [PSI:MS] +is_a: MS:1002489 ! special processing + + +[Term] +id: MS:1003331 +name: noncovalently associated peptides spectrum identification item +def: "Noncovalently associated peptides spectrum identification item." [PSI:MS] +is_a: MS:1002508 ! crosslinking attribute +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:1003332 +name: identification based on multiple spectra +def: "Provides an identifier to encode identifications based on multiple spectra." [PSI:MS] +is_a: MS:1002345 ! PSM-level attribute +relationship: has_regexp MS:1003333 ! regular expression for encoding identifications based on multiple spectra. +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003333 +name: regular expression for encoding identifications based on multiple spectra. +def: "^(?[0-9]+)(?::(?P|C))?$" [PSI:MS] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003334 +name: parent term for PSM-level scores for identifications based on multiple spectra +def: "Parent term for PSM-level scores for identifications based on multiple spectra." [PSI:MS] +is_a: MS:1002347 ! PSM-level identification statistic +is_a: MS:1002483 ! PSM-level statistical threshold +relationship: has_regexp MS:1003335 ! regular expression for PSM-level scores for identifications based on multiple spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003335 +name: regular expression for PSM-level scores for identifications based on multiple spectra +def: "^(?[0-9]+):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$" [PSI:MS] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003336 +name: posterior error probability from identification based on multiple spectra +def: "PEP score for identifications based on multiple spectra." [PSI:MS] +is_a: MS:1003334 ! Parent term for PSM-level scores for identifications based on multiple spectra +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003337 +name: crosslinked PSM-level global FDR +def: "Estimation of the global false discovery rate of crosslinked peptide spectrum matches." [PSI:MS] +is_a: MS:1002701 ! PSM-level result list statistic +is_a: MS:1002483 ! PSM-level statistical threshold +is_a: MS:1002664 ! interaction score derived from crosslinking +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003338 +name: peptide-pair sequence-level global FDR +def: "Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS] +is_a: MS:1002703 ! peptide sequence-level result list statistic +is_a: MS:1002484 ! peptide-level statistical threshold +is_a: MS:1002664 ! interaction score derived from crosslinking +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003339 +name: peptide-pair passes threshold +def: "Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS] +is_a: MS:1001105 ! peptide sequence-level identification attribute +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003340 +name: residue-pair passes threshold +def: "Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI)." [PSI:MS] +is_a: MS:1001060 ! quality estimation method details +relationship: has_regexp MS:1003342 ! regular expression for whether interaction score derived from crosslinking passes threshold +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003341 +name: protein-protein interaction passes threshold +def: "Protein-protein interaction passes threshold." [PSI:MS] +is_a: MS:1001060 ! quality estimation method details +relationship: has_regexp MS:1003342 ! regular expression for whether interaction score derived from crosslinking passes threshold +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003342 +name: regular expression for whether interaction score derived from crosslinking passes threshold +def: "^((?[0-9]+):(?true|false))$" [PSI:MS] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003343 +name: FDR applied separately to self crosslinks and protein heteromeric crosslinks +def: "States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences)." [PSI:MS] +is_a: MS:1002489 ! special processing +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: MS:1003344 +name: residue-pair ref +def: "Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI)." [PSI:MS] +is_a: MS:1002508 ! crosslinking attribute +relationship: has_regexp MS:1003345 ! regular expression for residue-pair ref +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003345 +name: regular expression for residue-pair ref +def: "^(([0-9]+).(a|b))$" [PSI:MS] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003346 +name: cleavable crosslinker stub +def: "This term indicates that a given protein modification is a derivative of a cleavable crosslinker." [PSI:MS] +is_a: MS:1001471 ! peptide modification details + +[Term] +id: MS:1003347 +name: Unimod derivative code +def: "The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’." [PSI:MS] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003348 +name: proteomics +def: "large-scale study of proteins and proteomes." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:1003349 +name: affinity proteomics +def: "large-scale study of proteins and proteomes via the use of affinity reagents." [PSI:MS] +is_a: MS:1003348 ! proteomics + +[Term] +id: MS:1003350 +name: mass spectrometry proteomics +def: "large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments." [PSI:MS] +is_a: MS:1003348 ! proteomics + +[Term] +id: MS:1003351 +name: top-down proteomics +def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins." [PSI:MS] +is_a: MS:1003350 ! mass spectrometry proteomics + +[Term] +id: MS:1003352 +name: native top-down proteomics +def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins." [PSI:MS] +is_a: MS:1003351 ! top-down proteomics + +[Term] +id: MS:1003353 +name: non-native top-down proteomics +def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins." [PSI:MS] +is_a: MS:1003351 ! top-down proteomics + +[Term] +id: MS:1003354 +name: middle-down proteomics +def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins." [PSI:MS] +is_a: MS:1003350 ! mass spectrometry proteomics + +[Term] +id: MS:1003355 +name: bottom-up proteomics +def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins." [PSI:MS] +is_a: MS:1003350 ! mass spectrometry proteomics + +[Term] +id: MS:1003356 +name: Orbitrap Ascend +def: "Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003357 +name: ANN-SoLo +def: "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart." [doi:10.1021/acs.jproteome.8b00359, doi:10.1021/acs.jproteome.9b00291] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003358 +name: XCorr rank +def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003359 +name: exact p-value +def: "A p-value for the XCorr score, calculated using dynamic programming." [PMID:24895379] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003360 +name: refactored XCorr +def: "A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003361 +name: res-ev score +def: "The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003362 +name: res-ev rank +def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003363 +name: res-ev p-value +def: "The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003364 +name: combined p-value +def: "A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003365 +name: combined p-value rank +def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003366 +name: tailor score +def: "A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum." [PMID:32175744] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003367 +name: monoisotopic mass deisotoping +def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000033 ! deisotoping + +[Term] +id: MS:1003368 +name: most abundant mass deisotoping +def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000033 ! deisotoping + +[Term] +id: MS:1003369 +name: average mass deisotoping +def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000033 ! deisotoping + +[Term] +id: MS:1003370 +name: reduction to summed singly charged peak list +def: "The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003371 +name: SelexION compensation voltage +def: "The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer." [PSI:MS] +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003372 +name: specification document extension version +def: "The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies +relationship: has_regexp MS:1003384 ! semantic version regexp + +[Term] +id: MS:1003373 +name: mzIdentML extension version +def: "The versioning of an mzIdentML extension document." [PSI:PI] +is_a: MS:1003372 ! specification document extension version +relationship: part_of MS:1002073 ! mzIdentML format + +[Term] +id: MS:1003374 +name: Open Chromatography Binary OCB format +def: "ChemClipse/OpenChrom file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003375 +name: Conversion to OCB +def: "Conversion of a file format to Open Chromatography Binary OCB file format." [PSI:MS] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1003376 +name: ChemClipse +def: "ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH." [https://projects.eclipse.org/projects/science.chemclipse] +synonym: "chemclipse" EXACT [] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003377 +name: OpenChrom +def: "OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse." [PMID:20673335, DOI:10.1186/1471-2105-11-405, https://www.openchrom.net/] +synonym: "openchrom" EXACT [] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003378 +name: Orbitrap Astral +def: "Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003379 +name: asymmetric track lossless time-of-flight analyzer +def: "A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution." [PSI:MS] +synonym: "Astral" EXACT [] +is_a: MS:1000084 ! time-of-flight + +[Term] +id: MS:1003380 +name: Xevo G3 QTof +def: "Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003381 +name: ACQUITY RDa Detector +def: "Waters Corporation RDa time-of-flight mass detector." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003382 +name: waters_connect +def: "Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing." [PSI:MS] +is_a: MS:1000694 ! Waters software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003383 +name: timsTOF Ultra +def: "Bruker Daltonics' timsTOF Ultra." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003384 +name: semantic version regexp +def: "v?(\d+)\.(\d+)\.(\d+)(?:-(\S+))?" [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003385 +name: mzIdentML crosslinking extension document version +def: "The versioning of the crosslinking mzIdentML extension document." [PSI:PI] +is_a: MS:1003373 ! mzIdentML extension version +relationship: has_value_type xsd:string + +[Term] +id: MS:1003386 +name: Spectra +def: "Bioconductor package Spectra for mass spectrometry data representation and processing." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.Spectra] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003387 +name: MetaboAnnotation +def: "Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.MetaboAnnotation, https://doi.org/10.3390/metabo12020173, PMID:35208247] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003388 +name: CompoundDb +def: "Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.CompoundDb, https://doi.org/10.3390/metabo12020173, PMID:35208247] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1003207 ! library creation software + +[Term] +id: MS:1003389 +name: mzTab-M +def: "Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence." [PMID:30688441, PMID:31525911, https://www.psidev.info/mztab] +is_a: MS:1000914 ! tab delimited text format + +[Term] +id: MS:1003390 +name: crosslinker cleavage characteristics +def: "Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_regexp MS:1003391 ! crosslinker cleavage regular expression +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003391 +name: crosslinker cleavage regular expression +def: "^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$" [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003392 +name: search modification id +def: "A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003393 +name: search modification id ref +def: "A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003394 +name: SelexION separation voltage +def: "RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF." [PSI:MS] +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003395 +name: Q Exactive GC Orbitrap +def: "Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer." [PSI:MS] +is_a: MS:1000483 ! Thermo Fisher Scientific instrument model + +[Term] +id: MS:1003396 +name: 8890 GC/MS +def: "Agilent 8890 Gas Chromatograph System." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1003397 +name: timsTOF fleX MALDI-2 +def: "Bruker Daltonics' timsTOF fleX MALDI-2." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003398 +name: deconvoluted data +def: "The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file." [PSI:MS] +is_a: MS:1000524 ! data file content + +[Term] +id: MS:1003399 +name: quality control software +def: "Software that creates or manipulates QC-related data." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003400 +name: rmzqc +def: "An R package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/rmzqc] +is_a: MS:1003399 ! quality control software + +[Term] +id: MS:1003401 +name: jmzqc +def: "A Java package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/jmzqc] +is_a: MS:1003399 ! quality control software + +[Term] +id: MS:1003402 +name: pymzqc +def: "A Python package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/pymzqc] +is_a: MS:1003399 ! quality control software + +[Term] +id: MS:1003403 +name: InChI +def: "IUPAC International Chemical Identifier." [PMID:26136848] +is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1000867 ! structural formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003404 +name: timsTOF HT +def: "Bruker Daltonics' timsTOF HT." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003405 +name: mzRecal +def: "MS1 recalibration using identified peptides as internal calibrants." [DOI:10.1093/bioinformatics/btab056, PMID:33538780, https://github.com/524D/mzrecal] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003406 +name: spectrum clustering software +def: "Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1003409 +name: Stellar +def: "Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:4000000 +name: PSI-MS CV Quality Control Vocabulary +def: "PSI Quality Control controlled vocabulary term." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: MS:4000001 +name: QC metric +def: "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000002 +name: QC metric value type +def: "The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000003 +name: single value +def: "Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS] +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000004 +name: n-tuple +def: "Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable)." [PSI:MS] +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000005 +name: table +def: "Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS] +comment: The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns. +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000006 +name: matrix +def: "A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable)." [PSI:MS] +comment: The actual structure of the matrix is defined in the mzQC specification document. +is_a: MS:4000002 ! QC metric value type + +[Term] +id: MS:4000007 +name: QC metric category +def: "Categorization of the QC metric." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000008 +name: ID based metric +def: "QC metric based on identification results." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000009 +name: ID free metric +def: "QC metric not based on identification results." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000010 +name: quantification based metric +def: "QC metric based on quantification results." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000012 +name: single run based metric +def: "QC metric calculated from a single run (e.g. one .raw file)." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000013 +name: multiple runs based metric +def: "QC metric calculated from multiple runs (e.g. multiple .raw files)." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000014 +name: single spectrum based metric +def: "QC metric calculated from a single spectrum." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000015 +name: multiple spectra based metric +def: "QC metric calculated from multiple spectra." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000016 +name: retention time metric +def: "QC metric related to retention time." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000017 +name: chromatogram metric +def: "QC metric related to a chromatogram." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000018 +name: XIC metric +def: "QC metric related to an extracted ion chromatogram." [PSI:MS] +is_a: MS:4000017 ! chromatogram metric + +[Term] +id: MS:4000019 +name: MS metric +def: "QC metric related to the mass spectrometry acquisition." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000020 +name: ion source metric +def: "QC metric related to events in the ion source." [PSI:MS] +is_a: MS:4000019 ! MS metric + +[Term] +id: MS:4000021 +name: MS1 metric +def: "QC metric based on MS1 events." [PSI:MS] +is_a: MS:4000019 ! MS metric + +[Term] +id: MS:4000022 +name: MS2 metric +def: "QC metric based on MS2 events." [PSI:MS] +is_a: MS:4000019 ! MS metric + +[Term] +id: MS:4000023 +name: sample preparation metric +def: "QC metric related to the sample preparation." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000024 +name: environment metric +def: "QC metric related to measurements of the ambient environment, such as the laboratory." [PSI:MS] +is_a: MS:4000001 ! QC metric + +[Term] +id: MS:4000050 +name: XIC50 fraction +def: "The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC." [PSI:MS] +comment: This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly. +synonym: "XIC-WideFrac" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept UO:0000191 ! fraction + +[Term] +id: MS:4000051 +name: XIC-FWHM quantiles +def: "The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3." [PSI:MS] +synonym: "XIC-FWHM-Q1" RELATED [PMID:24494671] +synonym: "XIC-FWHM-Q2" RELATED [PMID:24494671] +synonym: "XIC-FWHM-Q3" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000018 ! XIC metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept MS:1000086 ! full width at half-maximum +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_units UO:0000010 ! second + +[Term] +id: MS:4000052 +name: XIC-Height quartile ratios +def: "The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3." [PSI:MS] +synonym: "XIC-Height-Q2" RELATED [PMID:24494671] +synonym: "XIC-Height-Q3" RELATED [PMID:24494671] +synonym: "XIC-Height-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000018 ! XIC metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept STATO:0000105 ! log signal intensity ratio +relationship: has_value_concept UO:0000191 ! fraction + +[Term] +id: MS:4000053 +name: chromatography duration +def: "The retention time duration of the chromatography in seconds." [PSI:MS] +comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. +synonym: "RT-Duration" RELATED [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C25330 ! Duration +relationship: has_units UO:0000010 ! second + +[Term] +id: MS:4000054 +name: TIC quarters RT fraction +def: "The interval when the respective quarter of the TIC accumulates divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. +synonym: "RT-TIC-Q1" RELATED [PMID:24494671] +synonym: "RT-TIC-Q2" RELATED [PMID:24494671] +synonym: "RT-TIC-Q3" RELATED [PMID:24494671] +synonym: "RT-TIC-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction + +[Term] +id: MS:4000055 +name: MS1 quarter RT fraction +def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. +synonym: "RT-MS-Q1" RELATED [PMID:24494671] +synonym: "RT-MS-Q2" RELATED [PMID:24494671] +synonym: "RT-MS-Q3" RELATED [PMID:24494671] +synonym: "RT-MS-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction + +[Term] +id: MS:4000056 +name: MS2 quarter RT fraction +def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. +synonym: "RT-MSMS-Q1" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q2" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q3" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction + +[Term] +id: MS:4000057 +name: MS1 TIC-change quartile ratios +def: "The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3" [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. +synonym: "MS1-TIC-Change-Q2" RELATED [PMID:24494671] +synonym: "MS1-TIC-Change-Q3" RELATED [PMID:24494671] +synonym: "MS1-TIC-Change-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept STATO:0000105 ! log signal intensity ratio + +[Term] +id: MS:4000058 +name: MS1 TIC quartile ratios +def: "The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. +synonym: "MS1-TIC-Q2" RELATED [PMID:24494671] +synonym: "MS1-TIC-Q3" RELATED [PMID:24494671] +synonym: "MS1-TIC-Q4" RELATED [PMID:24494671] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept STATO:0000105 ! log signal intensity ratio + +[Term] +id: MS:4000059 +name: number of MS1 spectra +def: "The number of MS1 events in the run." [PSI:MS] +comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. +synonym: "MS1-Count" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000060 +name: number of MS2 spectra +def: "The number of MS2 events in the run." [PSI:MS] +comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. +synonym: "MS2-Count" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000061 +name: MS1 density quantiles +def: "The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode." [PSI:MS] +synonym: "MS1-Density-Q1" RELATED [PMID:24494671] +synonym: "MS1-Density-Q2" RELATED [PMID:24494671] +synonym: "MS1-Density-Q3" RELATED [PMID:24494671] +synonym: "MS1 peak density distribution - quantiles" EXACT [] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C45781 ! Density +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000062 +name: MS2 density quantiles +def: "The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode." [PSI:MS] +synonym: "MS2-Density-Q1" RELATED [PMID:24494671] +synonym: "MS2-Density-Q2" RELATED [PMID:24494671] +synonym: "MS2-Density-Q3" RELATED [PMID:24494671] +synonym: "MS2 peak density distribution - quantiles" EXACT [] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C45781 ! Density +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000063 +name: MS2 known precursor charges fractions +def: "The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher." [PSI:MS] +comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. +synonym: "MS2-PrecZ-1" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-2" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-3" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-4" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-5" NARROW [PMID:24494671] +synonym: "MS2-PrecZ-more" NARROW [PMID:24494671] +synonym: "IS-3A" RELATED [PMID:19837981] +synonym: "IS-3B" RELATED [PMID:19837981] +synonym: "IS-3C" RELATED [PMID:19837981] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_column MS:1000041 ! charge state +relationship: has_column UO:0000191 ! fraction + +[Term] +id: MS:4000064 +name: MS2 unknown and likely precursor charges fractions +def: "The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states." [PSI:MS] +synonym: "MS2-PrecZ-likely-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-likely-multi" RELATED [PMID:24494671] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_column MS:1000041 ! charge state +relationship: has_column UO:0000191 ! fraction + +[Term] +id: MS:4000065 +name: fastest frequency for MS level 1 collection +def: "Fastest frequency for MS level 1 collection" [PSI:MS] +comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. +synonym: "MS1-Freq-Max" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000106 ! hertz + +[Term] +id: MS:4000066 +name: fastest frequency for MS level 2 collection +def: "Fastest frequency for MS level 2 collection" [PSI:MS] +comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. +synonym: "MS2-Freq-Max" EXACT [PMID:24494671] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000106 ! hertz + +[Term] +id: MS:4000067 +name: MS run duration +def: "The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000019 ! MS metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_value_concept NCIT:C25330 ! Duration +relationship: has_units UO:0000010 ! second + +[Term] +id: MS:4000068 +name: spectra half-TIC +def: "The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_optional_column MS:1003063 ! universal spectrum identifier +relationship: has_optional_column MS:1000767 ! native spectrum identifier format +relationship: has_column UO:0000191 ! fraction +relationship: has_relation MS:1000285 ! total ion current + +[Term] +id: MS:4000069 +name: m/z acquisition range +def: "Upper and lower limit of m/z precursor values at which MSn spectra are recorded." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. Based on the used MS instrument configuration, the values should be similar. Variations between measurements may arise when employing acquisition in DDA mode. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000019 ! MS metric +relationship: has_units MS:1000040 ! m/z +relationship: has_value_concept STATO:0000035 ! range + +[Term] +id: MS:4000070 +name: retention time acquisition range +def: "Upper and lower limit of retention time at which spectra are recorded." [PSI:MS] +comment: An unusual low range may indicate incomplete sampling and/or a premature or failed LC run. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_units UO:0000010 ! second +relationship: has_value_concept STATO:0000035 ! range + +[Term] +id: MS:4000071 +name: number of chromatograms +def: "The number of chromatograms recorded for the run." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000072 +name: observed mass accuracy +def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000014 ! single spectrum based metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_concept MS:1000014 ! accuracy + +[Term] +id: MS:4000073 +name: QC sample metric +def: "A QC metric based on a QC sample of known content." [PSI:MS] +is_a: MS:4000007 ! QC metric category + +[Term] +id: MS:4000074 +name: high complexity QC sample metric +def: "A QC metric based on a QC sample of known and high complexity content." [PSI:MS] +is_a: MS:4000073 ! QC sample metric + +[Term] +id: MS:4000075 +name: low complexity QC sample metric +def: "A QC metric based on a QC sample of known and low complexity content." [PSI:MS] +is_a: MS:4000073 ! QC sample metric + +[Term] +id: MS:4000076 +name: QC2 sample metric +def: "A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design." [PSI:MS, PMID:23088386, PMID:29324744] +comment: Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR' +is_a: MS:4000074 ! high complexity QC sample metric + +[Term] +id: MS:4000077 +name: QC1 sample metric +def: "A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design)." [PSI:MS, PMID:23088386, PMID:29324744] +comment: Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK' +is_a: MS:4000075 ! low complexity QC sample metric + +[Term] +id: MS:4000078 +name: QC2 sample mass accuracies +def: "Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000076 ! QC2 sample metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_column MS:1003169 ! proforma peptidoform sequence +relationship: has_column MS:4000072 ! observed mass accuracy + +[Term] +id: MS:4000079 +name: QC2 sample intensities +def: "Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000076 ! QC2 sample metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_column MS:1003169 ! proforma peptidoform sequence +relationship: has_optional_column MS:1001858 ! XIC area +relationship: has_optional_column MS:1001859 ! normalized XIC area +relationship: has_optional_column MS:1001844 ! MS1 feature area +relationship: has_optional_column MS:1001843 ! MS1 feature maximum intensity +relationship: has_optional_column MS:1003085 ! previous MSn-1 scan precursor intensity + +[Term] +id: MS:4000080 +name: QC non-metric term +def: "QC terms associated but not directly metrics themselves." [PSI:MS] +relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary + +[Term] +id: MS:4000081 +name: first principal component +def: "Data from the first principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "1st PC" EXACT [] + +[Term] +id: MS:4000082 +name: second principal component +def: "Data from the second principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "2nd PC" EXACT [] + +[Term] +id: MS:4000083 +name: third principal component +def: "Data from the third principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "3rd PC" EXACT [] + +[Term] +id: MS:4000084 +name: fourth principal component +def: "Data from the fourth principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "4th PC" EXACT [] + +[Term] +id: MS:4000085 +name: fifth principal component +def: "Data from the fifth principal component of a PCA." [PSI:MS] +relationship: has_value_concept NCIT:C60694 ! Principal Component +is_a: MS:4000080 ! QC non-metric term +synonym: "5th PC" EXACT [] + +[Term] +id: MS:4000086 +name: mzQC input reference +def: "Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:4000087 +name: mzQC plot label +def: "Used to supply alternative labels for plotting figures." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:4000088 +name: batch label +def: "Used to supply batch label information with any string value." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:4000089 +name: injection sequence label +def: "Used to supply injection sequence information with consecutive whole numbers." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: MS:4000090 +name: principal component analysis of MaxQuant's protein group raw intensities +def: "A table with the PCA results of MaxQuant's protein group raw intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"} +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component + +[Term] +id: MS:4000091 +name: principal component analysis of MaxQuant's protein group lfq intensities +def: "A table with the PCA results of MaxQuant's protein group lfq intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"} +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component + +[Term] +id: MS:4000092 +name: identified MS1 feature area principal component analysis result +def: "A table with the PCA results of identified MS1 feature areas." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component +relationship: has_optional_column MS:4000087 ! mzQC plot label +relationship: has_optional_column MS:4000088 ! batch label +relationship: has_optional_column MS:4000089 ! injection sequence label + +[Term] +id: MS:4000093 +name: unidentified MS1 feature area principal component analysis result +def: "A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component +relationship: has_optional_column MS:4000087 ! mzQC plot label +relationship: has_optional_column MS:4000088 ! batch label +relationship: has_optional_column MS:4000089 ! injection sequence label + +[Term] +id: MS:4000094 +name: batch-corrected identified MS1 feature area principal component analysis result +def: "A table with the PCA results of identified MS1 feature areas after batch-correction." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_metric_category MS:4000013 ! multiple runs based metric +relationship: has_column MS:4000081 ! first principal component +relationship: has_column MS:4000086 ! mzQC input reference +relationship: has_optional_column MS:4000082 ! second principal component +relationship: has_optional_column MS:4000083 ! third principal component +relationship: has_optional_column MS:4000084 ! fourth principal component +relationship: has_optional_column MS:4000085 ! fifth principal component +relationship: has_optional_column MS:4000087 ! mzQC plot label +relationship: has_optional_column MS:4000088 ! batch label +relationship: has_optional_column MS:4000089 ! injection sequence label + +[Term] +id: MS:4000095 +name: slowest frequency for MS level 1 collection +def: "The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_units UO:0000106 ! hertz +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_metric_category MS:4000021 ! MS1 metric + +[Term] +id: MS:4000096 +name: slowest frequency for MS level 2 collection +def: "The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_units UO:0000106 ! hertz +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_metric_category MS:4000022 ! MS2 metric + +[Term] +id: MS:4000097 +name: MS1 signal jump (10x) count +def: "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans." [PSI:MS] +comment: An unusual high count of signal jumps or falls may indicate ESI stability issues. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_units UO:0000189 ! count unit +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term +synonym: "IS-1A" RELATED [] + +[Term] +id: MS:4000098 +name: MS1 signal fall (10x) count +def: "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans." [PSI:MS] +comment: An unusual high count of signal jumps or falls may indicate ESI stability issues. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_units UO:0000189 ! count unit +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term +synonym: "IS-1B" RELATED [] + +[Term] +id: MS:4000099 +name: number of empty MS1 scans +def: "Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] +comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_units UO:0000189 ! count unit +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:4000100 +name: number of empty MS2 scans +def: "Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] +comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_units UO:0000189 ! count unit +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:4000101 +name: number of empty MS3 scans +def: "Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] +comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_units UO:0000189 ! count unit +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: MS:4000102 +name: number of detected quantification data points +def: "The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000103 +name: number of identified quantification data points +def: "The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_value_type xsd:int ! The allowed value-type for this CV term +relationship: has_units UO:0000189 ! count unit + +[Term] +id: MS:4000104 +name: total ion currents +def: "Tabular representation of the total ion current detected in each of a series of mass spectra." [PSI:MS] +is_a: MS:4000005 ! table +is_a: MS:1000235 ! total ion current chromatogram +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_column MS:1000767 ! native spectrum identifier format +relationship: has_optional_column MS:1000894 ! retention time +relationship: has_optional_column MS:1003059 ! number of peaks +relationship: has_column MS:1000285 ! total ion current + +[Term] +id: MS:4000105 +name: ion injection parameters +def: "Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_column MS:1000767 ! native spectrum identifier format +relationship: has_column MS:1000927 ! ion injection time +relationship: has_optional_column MS:1000511! ms level +relationship: has_optional_column MS:1000465 ! scan polarity +relationship: has_optional_column MS:1000500 ! scan window upper limit +relationship: has_optional_column MS:1000501 ! scan window lower limit + +[Term] +id: MS:4000106 +name: MS1 frequency in equal parts of subsequent RT +def: "Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)" [PSI:MS] +comment: Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_units UO:0000106 ! hertz +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000107 +name: MS2 frequency in equal parts of subsequent RT +def: "Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)" [PSI:MS] +comment: Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_units UO:0000106 ! hertz +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000108 +name: MS1 peak density distribution mean +def: "From the distribution of peak densities in MS1, the mean" [PSI:MS] +comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000109 +name: MS1 peak density distribution sigma +def: "From the distribution of peak densities in MS1, the sigma value" [PSI:MS] +comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000110 +name: MS1 peak density distribution low outliers +def: "From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000111 +name: MS1 peak density distribution high outliers +def: "From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000112 +name: MS2 peak density distribution mean +def: "From the distribution of peak densities in MS2, the mean" [PSI:MS] +comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000113 +name: MS2 peak density distribution sigma +def: "From the distribution of peak densities in MS2, the sigma value" [PSI:MS] +comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000114 +name: MS2 peak density distribution low outliers +def: "From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000115 +name: MS2 peak density distribution high outliers +def: "From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000116 +name: MS2 precursor intensity distribution +def: "From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3." [PSI:MS] +comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000117 +name: MS2 precursor intensity distribution mean +def: "From the distribution of MS2 precursor intensities, the mean" [PSI:MS] +comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000118 +name: MS2 precursor intensity distribution sigma +def: "From the distribution of MS2 precursor intensities, the sigma value" [PSI:MS] +comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000119 +name: MS2 precursor intensity distribution low outliers +def: "From the distribution of precursor intensities, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000120 +name: MS2 precursor intensity distribution high outliers +def: "From the distribution of precursor intensities, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000121 +name: MS1 signal-to-noise ratio quantiles +def: "From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] +comment: The Signal-to-noise ratio in MS1 distribution can provide insight to the presence of nuisance factors. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000122 +name: MS1 signal-to-noise ratio mean +def: "From the distribution of signal-to-noise ratio in MS1, the mean" [PSI:MS] +comment: The signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000123 +name: MS1 signal-to-noise ratio sigma +def: "From the distribution of signal-to-noise ratio in MS1, the sigma value" [PSI:MS] +comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000124 +name: MS1 signal-to-noise ratio low outliers +def: "From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000125 +name: MS1 signal-to-noise ratio high outliers +def: "From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000126 +name: MS2 signal-to-noise ratio quantiles +def: "From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] +comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000127 +name: MS2 signal-to-noise ratio mean +def: "From the distribution of signal-to-noise ratio in MS2, the mean" [PSI:MS] +comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000128 +name: MS2 signal-to-noise ratio sigma +def: "From the distribution of signal-to-noise ratio in MS2, the sigma value" [PSI:MS] +comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000129 +name: MS2 signal-to-noise ratio low outliers +def: "From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000130 +name: MS2 signal-to-noise ratio high outliers +def: "From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000131 +name: MS1 ion collection time quantiles +def: "From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000132 +name: MS1 ion collection time mean +def: "From the distribution of ion injection times (MS:1000927) for MS1, the mean" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000133 +name: MS1 ion collection time sigma +def: "From the distribution of ion injection times (MS:1000927) for MS1, the sigma value" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000134 +name: MS1 ion collection time low outliers +def: "From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000135 +name: MS1 ion collection time high outliers +def: "From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000136 +name: MS2 ion collection time quantiles +def: "From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000137 +name: MS2 ion collection time mean +def: "From the distribution of ion injection times (MS:1000927) for MS2, the mean" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000138 +name: MS2 ion collection time sigma +def: "From the distribution of ion injection times (MS:1000927) for MS2, the sigma value" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000139 +name: MS2 ion collection time low outliers +def: "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000140 +name: MS2 ion collection time high outliers +def: "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold" [PSI:MS] +comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_units UO:0000028 ! millisecond +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000141 +name: outlier threshold criterion +def: "The definition of the outlier criteria applied." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term + +[Term] +id: MS:4000142 +name: Tukey's fence +def: "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000143 +name: Tukey's fence high outliers +def: "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000144 +name: Tukey's fence low outliers +def: "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000145 +name: Z-score threshold +def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000146 +name: Z-score threshold high outliers +def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000147 +name: Z-score threshold low outliers +def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000148 +name: algorithmical threshold +def: "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used." [PSI:MS] +is_a: MS:4000141 ! outlier threshold criterion + +[Term] +id: MS:4000149 +name: iRT calibration formula +def: "A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc." [PSI:MS] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000150 +name: iRT calibration adjusted r-squared +def: "The goodness of fit statistic between observed retention times and iRT calibrated retention times." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000151 +name: MsQuality +def: "MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data." [DOI:10.1101/2023.05.12.540477, https://github.com/tnaake/MsQuality/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:4000152 +name: MS2 precursor median m/z of identified quantification data points +def: "Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The m/z distribution informs about the dynamic range of the acquisition. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:4000153 +name: interquartile RT period for identified quantification data points +def: "The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_units UO:0000010 ! second +synonym: "C-2A" RELATED [PMID:19837981] + +[Term] +id: MS:4000154 +name: rate of the interquartile RT period for identified quantification data points +def: "The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher rates may indicate a more efficient sampling and identification. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_units UO:0000106 ! hertz +synonym: "C-2B" RELATED [PMID:19837981] + +[Term] +id: MS:4000155 +name: area under TIC +def: "The area under the total ion chromatogram." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free +relationship: has_metric_category MS:4000017 ! chromatogram metric + +[Term] +id: MS:4000156 +name: area under TIC RT quantiles +def: "The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment may indicate differences in chromatographic performance, differences in the dynamic range and/or in the sample content. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free +relationship: has_metric_category MS:4000017 ! chromatogram metric + +[Term] +id: MS:4000157 +name: extent of identified MS2 precursor intensity +def: "Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS1-3A" RELATED [PMID:19837981] + +[Term] +id: MS:4000158 +name: median of TIC values in the RT range in which the middle half of quantification data points are identified +def: "Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric + +[Term] +id: MS:4000159 +name: median of TIC values in the shortest RT range in which half of the quantification data points are identified +def: "Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +synonym: "MS1-2B" RELATED [PMID:19837981] + +[Term] +id: MS:4000160 +name: MS2 precursor intensity range +def: "Minimum and maximum MS2 precursor intensity recorded." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free +relationship: has_metric_category MS:4000022 ! MS2 metric + +[Term] +id: MS:4000161 +name: identified MS2 precursor intensity distribution +def: "From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000162 +name: unidentified MS2 precursor intensity distribution +def: "From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000291 ! quantile +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000163 +name: identified MS2 precursor intensity distribution mean +def: "From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000164 +name: unidentified MS2 precursor intensity distribution mean +def: "From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000165 +name: identified MS2 precursor intensity distribution sigma +def: "From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000166 +name: unidentified MS2 precursor intensity distribution sigma +def: "From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000167 +name: ratio of 1+ over 2+ of all MS2 known precursor charges +def: "The ratio of 1+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] +comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3A" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] + +[Term] +id: MS:4000168 +name: ratio of 1+ over 2+ of identified MS2 known precursor charges +def: "The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3A" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] + +[Term] +id: MS:4000169 +name: ratio of 3+ over 2+ of all MS2 known precursor charges +def: "The ratio of 3+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3B" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] + +[Term] +id: MS:4000170 +name: ratio of 3+ over 2+ of identified MS2 known precursor charges +def: "The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3B" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] + +[Term] +id: MS:4000171 +name: ratio of 4+ over 2+ of all MS2 known precursor charges +def: "The ratio of 4+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3C" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] + +[Term] +id: MS:4000172 +name: ratio of 4+ over 2+ of identified MS2 known precursor charges +def: "The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3C" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] + +[Term] +id: MS:4000173 +name: mean MS2 precursor charge in all spectra +def: "Mean MS2 precursor charge in all spectra" [PSI:MS] +comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000174 +name: mean MS2 precursor charge in identified spectra +def: "Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000175 +name: median MS2 precursor charge in all spectra +def: "Median MS2 precursor charge in all spectra" [PSI:MS] +comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000176 +name: median MS2 precursor charge in identified spectra +def: "Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000177 +name: contaminant protein abundance fraction +def: "The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database)." [PSI:MS] +comment: "High values may indicate a sample handling issue, and/or insufficient sample concentration." +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_order MS:1002109 ! lower score better +synonym: "PG: Contaminants" NARROW [] + +[Term] +id: MS:4000178 +name: precursor ppm deviation mean +def: "The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_value_concept MS:1000014 ! accuracy +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000179 +name: precursor ppm deviation sigma +def: "The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_value_concept MS:1000830 ! precision +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000180 +name: table of missed cleavage counts +def: "The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_column MS:1003044 ! number of missed cleavages +relationship: has_column NCIT:C150827 ! Number of Occurrences + +[Term] +id: MS:4000181 +name: identified MS2 quarter RT fraction +def: "The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction +synonym: "RT-MSMS-Q1" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q2" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q3" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q4" RELATED [PMID:24494671] + +[Term] +id: MS:1003407 +name: Scout +def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003408 +name: Scout score +def: "Scout identification search engine score" [PSI:MS] +is_a: MS:1003407 ! PSM-level search engine specific statistic +relationship: has_order MS:1003407 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000001 +name: PEFF CV term +def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies + +[Term] +id: PEFF:0000002 +name: PEFF file header section term +def: "CV term that may appear in a PEFF file header section." [PSI:PEFF] +is_a: PEFF:0000001 ! PEFF CV term + +[Term] +id: PEFF:0000003 +name: PEFF file sequence entry term +def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF] +is_a: PEFF:0000001 ! PEFF CV term + +[Term] +id: PEFF:0000008 +name: DbName +def: "PEFF keyword for the sequence database name." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000009 +name: Prefix +def: "PEFF keyword for the sequence database prefix." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000010 +name: DbDescription +def: "PEFF keyword for the sequence database short description." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000011 +name: Decoy +def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000012 +name: DbSource +def: "PEFF keyword for the source of the database file." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000013 +name: DbVersion +def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000014 +name: DbDate +def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF] +comment: This term was obsoleted. +is_a: PEFF:0000002 ! PEFF file header section term +is_obsolete: true + +[Term] +id: PEFF:0000015 +name: NumberOfEntries +def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000016 +name: Conversion +def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000017 +name: SequenceType +def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000018 +name: SpecificKey +def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000019 +name: SpecificValue +def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000020 +name: DatabaseDescription +def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000021 +name: GeneralComment +def: "PEFF keyword for a general comment." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000022 +name: ProteoformDb +def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000023 +name: OptionalTagDef +def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0000024 +name: HasAnnotationIdentifiers +def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF] +is_a: PEFF:0000002 ! PEFF file header section term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001001 +name: DbUniqueId +def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF] +comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. +is_a: PEFF:0000003 ! PEFF file sequence entry term +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001002 +name: PName +def: "PEFF keyword for the protein full name." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001003 +name: NcbiTaxId +def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001004 +name: TaxName +def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001005 +name: GName +def: "PEFF keyword for the gene name." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001006 +name: Length +def: "PEFF keyword for the sequence length." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001007 +name: SV +def: "PEFF keyword for the sequence version." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001008 +name: EV +def: "PEFF keyword for the entry version." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001009 +name: PE +def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:int ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001010 +name: Processed +def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001011 +name: Variant +def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] +comment: This term was made obsolete in favor of VariantSimple and VariantComplex. +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +is_obsolete: true +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001012 +name: ModResPsi +def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001013 +name: ModRes +def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001014 +name: AltAC +def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001015 +name: SeqStatus +def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001016 +name: CC +def: "PEFF keyword for the entry associated comment." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001017 +name: KW +def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001018 +name: GO +def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001019 +name: XRef +def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001020 +name: mature protein +def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001021 +name: signal peptide +def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001022 +name: transit peptide +def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001023 +name: Conflict +def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001024 +name: Crc64 +def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001025 +name: Domain +def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001026 +name: ID +def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001027 +name: ModResUnimod +def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001028 +name: VariantSimple +def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001029 +name: VariantComplex +def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001030 +name: Proteoform +def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001031 +name: DisulfideBond +def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001032 +name: PEFF molecule processing keyword +def: "PEFF keyword describing the type of processing event being described." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term + +[Term] +id: PEFF:0001033 +name: Comment +def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF] +is_a: PEFF:0000003 ! PEFF file sequence entry term +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001034 +name: propeptide +def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:0001035 +name: initiator methionine +def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] +is_a: PEFF:0001032 ! PEFF molecule processing keyword +relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: PEFF:1002001 +name: regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment +def: "([0-9]+|[A-Z*](|.+)?)." [PSI:PEFF] +is_a: MS:1002479 ! regular expression + +[Term] +id: PEFF:1002002 +name: regular expression for PEFF molecular sequence type +def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] +is_a: MS:1002479 ! regular expression + +[Term] +id: PEFF:1002003 +name: regular expression for PEFF sequence status +def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] +is_a: MS:1002479 ! regular expression + + +[Term] +id: UO:0000000 +name: unit +namespace: unit.ontology +def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] +created_by: george gkoutos + +[Term] +id: UO:0000001 +name: length unit +namespace: unit.ontology +def: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001708 +created_by: george gkoutos + +[Term] +id: UO:0000002 +name: mass unit +namespace: unit.ontology +def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0000125 +relationship: is_unit_of PATO:0000128 +created_by: george gkoutos + +[Term] +id: UO:0000003 +name: time unit +namespace: unit.ontology +alt_id: UO:0000149 +def: "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] +subset: unit_group_slim +synonym: "time derived unit" EXACT [] +is_a: UO:0000000 +relationship: is_unit_of PATO:0000165 +relationship: is_unit_of PATO:0001309 +created_by: george gkoutos + +[Term] +id: UO:0000005 +name: temperature unit +namespace: unit.ontology +alt_id: UO:0000126 +def: "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] +subset: unit_group_slim +synonym: "temperature derived unit" EXACT [] +is_a: UO:0000000 +relationship: is_unit_of PATO:0000146 +created_by: george gkoutos + +[Term] +id: UO:0000008 +name: meter +namespace: unit.ontology +def: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] +subset: unit_slim +synonym: "m" EXACT [] +synonym: "metre" EXACT [] +is_a: UO:0000001 +is_a: UO:0000045 +created_by: george gkoutos + +[Term] +id: UO:0000010 +name: second +namespace: unit.ontology +def: "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] +subset: unit_slim +synonym: "s" EXACT [] +is_a: UO:0000003 +is_a: UO:0000045 +created_by: george gkoutos + +[Term] +id: UO:0000012 +name: kelvin +namespace: unit.ontology +def: "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] +subset: unit_slim +synonym: "K" EXACT [] +is_a: UO:0000005 +is_a: UO:0000045 +created_by: george gkoutos + +[Term] +id: UO:0000017 +name: micrometer +namespace: unit.ontology +def: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] +subset: unit_slim +synonym: "micrometre" EXACT [] +synonym: "micron" EXACT [] +synonym: "um" EXACT [] +is_a: UO:0000001 +created_by: george gkoutos + +[Term] +id: UO:0000018 +name: nanometer +namespace: unit.ontology +def: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] +subset: unit_slim +synonym: "nanometre" EXACT [] +synonym: "nm" EXACT [] +is_a: UO:0000001 +created_by: george gkoutos + +[Term] +id: UO:0000021 +name: gram +namespace: unit.ontology +def: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST] +subset: unit_slim +synonym: "g" EXACT [] +is_a: UO:0000002 +created_by: george gkoutos + +[Term] +id: UO:0000027 +name: degree Celsius +namespace: unit.ontology +def: "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] +subset: unit_slim +synonym: "C" EXACT [] +is_a: UO:0000005 +created_by: george gkoutos + +[Term] +id: UO:0000028 +name: millisecond +namespace: unit.ontology +def: "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] +subset: unit_slim +synonym: "ms" EXACT [] +is_a: UO:0000003 +created_by: george gkoutos + +[Term] +id: UO:0000031 +name: minute +namespace: unit.ontology +def: "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "min" EXACT [] +is_a: UO:0000003 +created_by: george gkoutos + +[Term] +id: UO:0000045 +name: base unit +namespace: unit.ontology +def: "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000047 +name: area unit +namespace: unit.ontology +def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001709 +created_by: george gkoutos + +[Term] +id: UO:0000052 +name: mass density unit +namespace: unit.ontology +def: "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] +subset: unit_group_slim +synonym: "mass per unit volume" EXACT [] +is_a: UO:0000182 +relationship: is_unit_of PATO:0001353 +created_by: george gkoutos + +[Term] +id: UO:0000095 +name: volume unit +namespace: unit.ontology +def: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001710 +created_by: george gkoutos + +[Term] +id: UO:0000098 +name: milliliter +namespace: unit.ontology +def: "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] +subset: unit_slim +synonym: "millilitre" EXACT [] +synonym: "ml" EXACT [] +is_a: UO:0000095 +created_by: george gkoutos + +[Term] +id: UO:0000105 +name: frequency unit +namespace: unit.ontology +def: "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0000044 +created_by: george gkoutos + +[Term] +id: UO:0000106 +name: hertz +namespace: unit.ontology +def: "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST] +subset: unit_slim +synonym: "Hz" EXACT [] +synonym: "s^1" EXACT [] +is_a: UO:0000105 +created_by: george gkoutos + +[Term] +id: UO:0000109 +name: pressure unit +namespace: unit.ontology +def: "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001025 +created_by: george gkoutos + +[Term] +id: UO:0000110 +name: pascal +namespace: unit.ontology +def: "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST] +subset: unit_slim +synonym: "Pa" EXACT [] +is_a: UO:0000109 +created_by: george gkoutos + +[Term] +id: UO:0000111 +name: energy unit +namespace: unit.ontology +def: "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001021 +relationship: is_unit_of PATO:0001026 +created_by: george gkoutos + +[Term] +id: UO:0000112 +name: joule +namespace: unit.ontology +def: "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST] +subset: unit_slim +synonym: "J" EXACT [] +is_a: UO:0000111 +created_by: george gkoutos + +[Term] +id: UO:0000121 +name: angle unit +namespace: unit.ontology +def: "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0000133 +created_by: george gkoutos + +[Term] +id: UO:0000122 +name: plane angle unit +namespace: unit.ontology +def: "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000121 +created_by: george gkoutos + +[Term] +id: UO:0000150 +name: nanosecond +namespace: unit.ontology +def: "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] +subset: unit_slim +synonym: "ns" EXACT [] +is_a: UO:0000003 +created_by: george gkoutos + +[Term] +id: UO:0000166 +name: parts per notation unit +namespace: unit.ontology +def: "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000186 +created_by: george gkoutos + +[Term] +id: UO:0000169 +name: parts per million +namespace: unit.ontology +def: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG] +subset: unit_slim +synonym: "10^[-6]" EXACT [] +synonym: "ppm" EXACT [] +is_a: UO:0000166 +created_by: george gkoutos + +[Term] +id: UO:0000175 +name: gram per liter +namespace: unit.ontology +def: "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] +subset: unit_slim +synonym: "g/L" EXACT [] +synonym: "gram per litre" EXACT [] +is_a: UO:0000052 +created_by: george gkoutos + +[Term] +id: UO:0000182 +name: density unit +namespace: unit.ontology +def: "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001019 +created_by: george gkoutos + +[Term] +id: UO:0000185 +name: degree +namespace: unit.ontology +def: "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] +subset: unit_slim +is_a: UO:0000122 +created_by: george gkoutos + +[Term] +id: UO:0000186 +name: dimensionless unit +namespace: unit.ontology +def: "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000187 +name: percent +namespace: unit.ontology +def: "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] +subset: unit_group_slim +synonym: "%" EXACT [] +is_a: UO:0000190 +created_by: george gkoutos + +[Term] +id: UO:0000189 +name: count unit +namespace: unit.ontology +def: "A dimensionless unit which denotes a simple count of things." [MGED:MGED] +subset: unit_group_slim +synonym: "count" EXACT [] +is_a: UO:0000186 +created_by: george gkoutos + +[Term] +id: UO:0000190 +name: ratio +namespace: unit.ontology +def: "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000186 +created_by: george gkoutos + +[Term] +id: UO:0000191 +name: fraction +namespace: unit.ontology +def: "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000190 +created_by: george gkoutos + +[Term] +id: UO:0000217 +name: electric potential difference unit +namespace: unit.ontology +def: "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +relationship: is_unit_of PATO:0001464 +created_by: george gkoutos + +[Term] +id: UO:0000218 +name: volt +namespace: unit.ontology +def: "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "V" EXACT [] +is_a: UO:0000217 +created_by: george gkoutos + +[Term] +id: UO:0000221 +name: dalton +namespace: unit.ontology +def: "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "amu" EXACT [] +synonym: "Da" EXACT [] +synonym: "u" EXACT [] +synonym: "unified atomic mass unit" EXACT [] +is_a: UO:0000002 +created_by: george gkoutos + +[Term] +id: UO:0000222 +name: kilodalton +namespace: unit.ontology +def: "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "kDa" EXACT [] +is_a: UO:0000002 +created_by: george gkoutos + +[Term] +id: UO:0000227 +name: magnetic flux density unit +namespace: unit.ontology +def: "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet] +subset: unit_group_slim +synonym: "B" EXACT [] +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000228 +name: tesla +namespace: unit.ontology +def: "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet] +subset: unit_slim +synonym: "T" EXACT [] +synonym: "Wb/m2" EXACT [] +is_a: UO:0000227 +created_by: george gkoutos + +[Term] +id: UO:0000266 +name: electronvolt +namespace: unit.ontology +def: "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia] +subset: unit_slim +synonym: "electron volt" EXACT [] +synonym: "eV" EXACT [] +is_a: UO:0000111 +created_by: george gkoutos + +[Term] +id: UO:0000267 +name: electric field strength unit +namespace: unit.ontology +def: "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] +subset: unit_group_slim +synonym: "E-field strength " EXACT [] +is_a: UO:0000000 +created_by: george gkoutos +creation_date: 2009-03-03T12:23:16Z + +[Term] +id: UO:0000268 +name: volt per meter +namespace: unit.ontology +def: "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] +subset: unit_slim +synonym: "V/m" EXACT [] +synonym: "volt per metre" EXACT [] +is_a: UO:0000267 +created_by: george gkoutos +creation_date: 2009-03-03T12:28:17Z + +[Term] +id: UO:0000269 +name: absorbance unit +namespace: unit.ontology +def: "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance] +subset: unit_slim +synonym: "AU" EXACT [] +is_a: UO:0000186 +created_by: george gkoutos +creation_date: 2009-07-14T12:33:48Z + +[Term] +id: UO:0000270 +name: volumetric flow rate unit +namespace: unit.ontology +def: "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] +subset: unit_group_slim +is_a: UO:0000000 +created_by: george gkoutos + +[Term] +id: UO:0000271 +name: microliters per minute +namespace: unit.ontology +def: "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG] +subset: unit_slim +synonym: "microlitres per minute" EXACT [] +synonym: "uL/min" EXACT [] +is_a: UO:0000270 +relationship: is_unit_of PATO:0001574 +created_by: george gkoutos + +[Term] +id: UO:0000324 +name: square angstrom +namespace: unit.ontology +def: "An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long." [UOC:GVG] +synonym: "A^[2]" RELATED [] +is_a: UO:0000047 +created_by: gkoutos +creation_date: 2013-06-27T05:06:40Z + + From 957b20e0ffb86e57e88e1e7376292f30a7b3891e Mon Sep 17 00:00:00 2001 From: julianu Date: Wed, 10 Jul 2024 14:47:47 +0200 Subject: [PATCH 3/4] changing and updating logger --- .../compiler/parser/MzIdentMLFileParser.java | 88 ++++++++----------- 1 file changed, 37 insertions(+), 51 deletions(-) diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java index a78fc07..3633ce5 100755 --- a/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java +++ b/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java @@ -12,7 +12,8 @@ import de.mpc.pia.tools.obo.OBOMapper; import org.apache.commons.text.StringEscapeUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.biojava.nbio.ontology.Term; import org.biojava.nbio.ontology.Triple; import uk.ac.ebi.jmzidml.model.mzidml.*; @@ -35,7 +36,7 @@ class MzIdentMLFileParser { /** logger for this class */ - private static final Logger LOGGER = Logger.getLogger(MzIdentMLFileParser.class); + private static final Logger LOGGER = LogManager.getLogger(); /** the used PIA compiler */ @@ -136,10 +137,10 @@ private boolean parseFile(String name, String fileName) { // get the AnalysisCollection:SpectrumIdentification for the SpectrumIdentificationLists AnalysisCollection analysisCollection = unmarshaller.unmarshal(AnalysisCollection.class); - LOGGER.debug("scanning analysisCollection: " + analysisCollection - + "\n\tgetSpectrumIdentification " + analysisCollection.getSpectrumIdentification() - + "\n\tgetProteinDetection " + analysisCollection.getProteinDetection() - ); + LOGGER.debug("scanning analysisCollection: {} " + + "\n\tgetSpectrumIdentification {}" + + "\n\tgetProteinDetection {}" , + analysisCollection, analysisCollection.getSpectrumIdentification(), analysisCollection.getProteinDetection()); for (SpectrumIdentification si : analysisCollection.getSpectrumIdentification()) { if (specIdLists.keySet().contains(si.getSpectrumIdentificationListRef())) { @@ -153,8 +154,7 @@ private boolean parseFile(String name, String fileName) { neededSpectraData.addAll(si.getInputSpectra().stream().map(InputSpectra::getSpectraDataRef).toList()); neededSearchDatabases.addAll(si.getSearchDatabaseRef().stream().map(SearchDatabaseRef::getSearchDatabaseRef).toList()); } else { - LOGGER.warn("file contains SpectrumIdentification (" - + si.getId() + ") without SpectrumIdentificationList!"); + LOGGER.warn("file contains SpectrumIdentification ({}) without SpectrumIdentificationList!", si.getId()); } } @@ -199,34 +199,20 @@ private boolean parseFile(String name, String fileName) { dbSequences = new HashMap<>(); for (DBSequence dbSeq : sc.getDBSequence()) { dbSequences.put(dbSeq.getId(), dbSeq); - - LOGGER.debug("added dbSequence: " + dbSeq.getId() + " -> " + dbSequences.get(dbSeq.getId())); } // get/hash the SequenceCollection:Peptides peptides = new HashMap<>(); for (uk.ac.ebi.jmzidml.model.mzidml.Peptide peptide: sc.getPeptide()) { peptides.put(peptide.getId(), peptide); - - LOGGER.debug("added peptide: " + peptide.getId() - + " -> " + peptides.get(peptide.getId()) - + "\n\tpeptideSequence " + peptide.getPeptideSequence() - ); } // get/hash the SequenceCollection:PeptideEvidences peptideEvidences = new HashMap<>(); for (PeptideEvidence pepEvidence : sc.getPeptideEvidence()) { peptideEvidences.put(pepEvidence.getId(), pepEvidence); - - LOGGER.debug("added pepEvidence: " + pepEvidence.getId() - + " -> " + peptideEvidences.get(pepEvidence.getId()) - + "\n\tdbSequenceRef " + pepEvidence.getDBSequenceRef() - + "\n\tdbSequence " + pepEvidence.getDBSequence() - ); } - boolean ok = true; // go through the SpectrumIdentificationList:SpectrumIdentificationResult:SpectrumIdentificationItem and build the PeptideSpectrumMatches, Accessions and Peptides @@ -238,10 +224,10 @@ private boolean parseFile(String name, String fileName) { } } - LOGGER.info("inserted new: \n\t" + - pepNr + " peptides\n\t" + - specNr + " peptide spectrum matches\n\t" + - accNr + " accessions"); + LOGGER.info("inserted new: \n" + + "\t{} peptides\n" + + "\t{} peptide spectrum matches\n" + + "\t{} accessions", pepNr, specNr, accNr); return ok; } @@ -258,7 +244,7 @@ private boolean createUnmarshaller(String name, String fileName) { File mzidFile = new File(fileName); if (!mzidFile.canRead()) { - LOGGER.error("could not read '" + fileName + "'."); + LOGGER.error("could not read '{}'.", fileName); return false; } @@ -266,7 +252,7 @@ private boolean createUnmarshaller(String name, String fileName) { InputFileParserFactory.InputFileTypes.MZIDENTML_INPUT.getFileSuffix()); unmarshaller = new MzIdentMLUnmarshaller(mzidFile); - LOGGER.debug("Version of mzIdentML file: " + unmarshaller.getMzIdentMLVersion()); + LOGGER.debug("Version of mzIdentML file: {}", unmarshaller.getMzIdentMLVersion()); return true; } @@ -336,7 +322,7 @@ private void checkEnzymeRegEx(Enzyme enzyme) { getAndSetEnzymeRegexFromOBO(oboID, enzyme); } else { // TODO: parse the enzyme regex from a userParam - LOGGER.error("unsupported enzyme: " + param.getName() + " / " + param.getValue()); + LOGGER.error("unsupported enzyme: {} / {}", param.getName(), param.getValue()); } } } else if ((enzyme.getSiteRegexp() != null) && enzyme.getSiteRegexp().contains(" ")) { @@ -410,7 +396,7 @@ private boolean addSpectrumIdentificationList(SpectrumIdentificationList specIDL } // go through all the SpectrumIdentificationResults and build the PSMs - LOGGER.debug("Processing " + specIDList.getSpectrumIdentificationResult().size() + " specIdResults"); + LOGGER.debug("Processing {} specIdResults", specIDList.getSpectrumIdentificationResult().size()); boolean ok = true; for (SpectrumIdentificationResult specIdRes : specIDList.getSpectrumIdentificationResult()) { ok = addSpectrumIdentificationResult(specIdRes, spectrumID, specIDListsDBRefs, specIDListsEnzymes, @@ -637,8 +623,7 @@ private boolean processSpectrumIdentificationItem(SpectrumIdentificationItem spe processModification(mod, sequence, psm); } } else { - LOGGER.warn("no peptide for the peptide_ref " + specIdItem.getPeptideRef() + - " in the SequenceCollection -> can't get Modifications for it."); + LOGGER.warn("no peptide for the peptide_ref {} in the SequenceCollection -> can't get Modifications for it.", specIdItem.getPeptideRef()); } // the PSM is finished here @@ -682,14 +667,13 @@ private Peptide parseSIIPeptideEvidences(List peptideEvidenc PeptideEvidence pepEvidence = peptideEvidences.get(pepEvRef.getPeptideEvidenceRef()); if (pepEvidence == null) { - LOGGER.error("PeptideEvidence " + pepEvRef.getPeptideEvidenceRef() + " not found!"); + LOGGER.error("PeptideEvidence {} not found!", pepEvRef.getPeptideEvidenceRef()); return null; } DBSequence dbSeq = dbSequences.get(pepEvidence.getDBSequenceRef()); if (dbSeq == null) { - LOGGER.error("DBSequence " + pepEvidence.getDBSequenceRef() - + " for pepEvidence " + pepEvidence.getId() + " not found!"); + LOGGER.error("DBSequence {} for pepEvidence {} not found!", pepEvidence.getDBSequenceRef(), pepEvidence.getId()); return null; } @@ -703,7 +687,7 @@ private Peptide parseSIIPeptideEvidences(List peptideEvidenc sequence = pepEvSequence; } else { if (!sequence.equals(pepEvSequence)) { - LOGGER.error("Different sequences found for a PSM: " + sequence + " != " + pepEvSequence); + LOGGER.error("Different sequences found for a PSM: {} != {}", sequence, pepEvSequence); return null; } } @@ -739,7 +723,7 @@ private static String getPeptideEvidenceSequence(Integer start, Integer end, LOGGER.error("No peptide sequence found for a peptide!"); } - if ((proteinSequence != null) && (peptide != null) && proteinSequence.trim().length() > 0) { + if ((start != null) && (end != null) && (proteinSequence != null) && (peptide != null) && proteinSequence.trim().length() > 0) { // some exporters get the start and stop of sequences wrong if (start-1 < 0) { start++; @@ -747,8 +731,7 @@ private static String getPeptideEvidenceSequence(Integer start, Integer end, String dbEvSeq = proteinSequence.substring(start-1, end); if ((dbEvSeq != null) && !dbEvSeq.equals(pepEvSequence)) { - LOGGER.warn("PSM sequence fromSearchDB differs to sequence from Peptide: " + - dbEvSeq + " != " + pepEvSequence + ". Only sequence from Peptide is used."); + LOGGER.warn("PSM sequence fromSearchDB differs to sequence from Peptide: {} != {}. Only sequence from Peptide is used.", dbEvSeq, pepEvSequence); } } @@ -785,10 +768,10 @@ private Accession addAccessionInformationFromPeptideEvidence(DBSequence dbSeq, S if (proteinSequence != null) { if ((acc.getDbSequence() != null) && !proteinSequence.equals(acc.getDbSequence())) { - LOGGER.warn("Different DBSequences found for same Accession, this is not suported!\n" + - "\t Accession: " + acc.getAccession() + - '\t' + dbSeq.getSeq() + '\n' + - '\t' + acc.getDbSequence()); + LOGGER.warn("Different DBSequences found for same Accession, this is not suported!\n" + + "\tAccession: {}" + + "\t{}\n" + + "\t!= {}", acc.getAccession(), dbSeq.getSeq(), acc.getDbSequence()); } else if (acc.getDbSequence() == null) { // found a sequence now acc.setDbSequence(proteinSequence); @@ -1087,7 +1070,7 @@ private static boolean addScoreFromParam(PeptideSpectrumMatch psm, UserParam use */ public static boolean checkFileType(String fileName) { boolean isMzIdentMLFile = false; - LOGGER.debug("checking whether this is an mzIdentML file: " + fileName); + LOGGER.debug("checking whether this is an mzIdentML file: {}", fileName); try (Stream stream = Files.lines(Paths.get(fileName))) { // read in the first 10, not empty lines @@ -1099,24 +1082,27 @@ public static boolean checkFileType(String fileName) { int idx = 0; // optional declaration - if (lines.get(idx).trim().matches("<\\?xml version=\"[0-9.]+\"( encoding=\"[^\"]+\"){0,1}( standalone=\\\"[^\\\"]+\\\"){0,1}\\?>")) { - LOGGER.debug("file has the XML declaration line:" + lines.get(idx)); + String line = lines.get(idx); + if (line.trim().matches("<\\?xml version=\"[0-9.]+\"( encoding=\"[^\"]+\")?( standalone=\\\"[^\\\"]+\\\")?\\?>")) { + LOGGER.debug("file has the XML declaration line: {}", line); idx++; } // optional stylesheet declaration - if (lines.get(idx).trim().matches("<\\?xml-stylesheet.+\\?>")) { - LOGGER.debug("file has the XML stylesheet line:" + lines.get(idx)); + line = lines.get(idx); + if (line.trim().matches("<\\?xml-stylesheet.+\\?>")) { + LOGGER.debug("file has the XML stylesheet line: {}", line); idx++; } // now the MzIdentML element must be next - if (lines.get(idx).trim().matches(" Date: Thu, 11 Jul 2024 13:36:30 +0200 Subject: [PATCH 4/4] removing useless dep --- pom.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/pom.xml b/pom.xml index 1bb23b3..bd256fe 100644 --- a/pom.xml +++ b/pom.xml @@ -315,13 +315,6 @@ commons-compress ${commons-compress.version} - io.airlift aircompressor