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support Proteome Discoverer for DDA modules #474

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2 of 4 tasks
mlocardpaulet opened this issue Dec 4, 2024 · 8 comments
Open
2 of 4 tasks

support Proteome Discoverer for DDA modules #474

mlocardpaulet opened this issue Dec 4, 2024 · 8 comments
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@mlocardpaulet
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DDA quantification - peptidoforms later

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@mlocardpaulet
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mlocardpaulet commented Dec 4, 2024 •
edited by RobbinBouwmeester
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I am on it:

  • make documentation (need to explain specific parsing rules for the fasta; export format)
  • make toml
  • parse input
  • parse params for public upload (and find what parameter file to use)
@mlocardpaulet mlocardpaulet self-assigned this Dec 4, 2024
@mlocardpaulet
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We still need to handle the column headers (sample names may change). I don't think that we can have a classical matching that would look for exact match in column headers.
The file .._StudyInformation.txt contains the information of raw file name <-> sample name. Maybe we can use this.

We also need to parse the parameter files. Right now I see 2:

  • pdConsensusWF is the consensus workflow with quantification, global validation etc...
  • pdProcessingWF is the one with the search parameters. So in theory there could be one per raw file. This could be an issue. But here we used the same for all the raw files.
    I think that we can definitely discuss with the developers if there is another global parameter file.
    Regarding how to parse them:
    The workflows are modular, so there will be a set of parameter per module. I will have a look at how to find the information we need.

@mlocardpaulet
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@RobbinBouwmeester:
I had a look, and I don't think that we can easily work with the pdProcessing/pdConsensusWF. We may want to contact the developers for help. I am happy to do so early next year.
Reasons:

  • I cannot find anywhere the Proteome Discoverer version
  • flexibility in workflows, and search engines makes it difficult to find the search-engine-specific parameter. Here are the examples for Mascot and Sequest (I am not sure that the ProcessingNodeNumber is always 3, don't think so):
<WorkflowNode ProcessingNodeNumber="3" ProcessingNodeName="Mascot" FriendlyName="Mascot" Description="Performs a Mascot search." MainVersion="1" MinorVersion="36" Guid="7643d5ae-af3b-40c7-9be3-da9413336c93" Category="Sequence Database Search" ParentProcessingNodeNumber="2" Comment="" Publisher="Thermo Scientific" NodeState="Created">
			<ProcessingNodeInterfaces>
				<ProcessingNodeInterface Kind="Functional" Name="IProcessingNode" />
				<ProcessingNodeInterface Kind="Functional" Name="IPeptideAssignerNode" />
			</ProcessingNodeInterfaces>
			<ConnectionPoints>
				<ConnectionPoint Direction="Outgoing" Multiplicity="Single" ConnectionRequirement="RequiredAtDesignTime" Mode="Manual" DisplayName="PSM Validation" ConnectionDataHandlingType="FileBased" ParentNodeConstraint="None">
					<DataContracts>
						<DataContract DataType="http://thermo.magellan.com/owl/DataTypes/Psms">
							<DataTypeAttributes>
								<DataTypeAttribute>http://thermo.magellan.com/owl/DataTypes/ScoredWithEValue</DataTypeAttribute>
								<DataTypeAttribute>http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore</DataTypeAttribute>
								<DataTypeAttribute>http://thermo.magellan.com/owl/DataTypes/WithDecoys</DataTypeAttribute>
							</DataTypeAttributes>
						</DataContract>
						<DataContract DataType="http://thermo.magellan.com/owl/DataTypes/Proteins">
							<DataTypeAttributes>
								<DataTypeAttribute>http://thermo.magellan.com/owl/DataTypes/WithDecoys</DataTypeAttribute>
							</DataTypeAttributes>
						</DataContract>
					</DataContracts>
				</ConnectionPoint>
				<ConnectionPoint Direction="Incoming" Multiplicity="Single" ConnectionRequirement="RequiredAtDesignTime" Mode="Manual" DisplayName="Spectrum Retrieval" ConnectionDataHandlingType="InMemory" ParentNodeConstraint="None">
					<DataContracts>
						<DataContract DataType="http://thermo.magellan.com/owl/DataTypes/MSnSpectra">
							<DataTypeAttributes />
						</DataContract>
					</DataContracts>
				</ConnectionPoint>
			</ConnectionPoints>
			<ProcessingNodeParameters>
				<ProcessingNodeParameter Name="Instrument" FriendlyName="Instrument" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="ESI FTMS HCD">ESI FTMS HCD</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="FragmentTolerance" FriendlyName="Fragment Mass Tolerance" Category="2. Tolerances" IsAdvanced="False" IntendedPurpose="FragmentMassTolerance" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="0.02 Da">0.02 Da</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UseNeutralAIons" FriendlyName="Use Neutral Loss A Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/A_IonsWithNeutralLosses" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UseNeutralBIons" FriendlyName="Use Neutral Loss B Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/B_IonsWithNeutralLosses" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UseNeutralYIons" FriendlyName="Use Neutral Loss Y Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/Y_IonsWithNeutralLosses" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UseNeutralZIons" FriendlyName="Use Neutral Loss Z Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/Z_IonsWithNeutralLosses" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieA" FriendlyName="Weight of A Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/A_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieB" FriendlyName="Weight of B Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/B_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieC" FriendlyName="Weight of C Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/C_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieD" FriendlyName="Weight of D Ions" Category="6. Ion Series" IsAdvanced="True" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/D_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieV" FriendlyName="Weight of V Ions" Category="6. Ion Series" IsAdvanced="True" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/V_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieW" FriendlyName="Weight of W Ions" Category="6. Ion Series" IsAdvanced="True" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/W_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieX" FriendlyName="Weight of X Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/X_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieY" FriendlyName="Weight of Y Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/Y_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieZ" FriendlyName="Weight of Z Ions" Category="6. Ion Series" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesToggle" PurposeDetails="IonSeriesPurpose/Z_Ions" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="SignificanceHigh" FriendlyName="Significance High" Category="1. Default Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="MascotPurposeDetails/SignificanceStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0.01">0.01</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="SignificanceMiddle" FriendlyName="Significance Middle" Category="1. Default Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="MascotPurposeDetails/SignificanceRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0.05">0.05</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DefaultStrictScoreThreshold" FriendlyName="Strict Score Threshold" Category="1. Default Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="PeptideValidationPurpose/DefaultStrictScoreThreshold" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="30">30</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DefaultRelaxedScoreThreshold" FriendlyName="Relaxed Score Threshold" Category="1. Default Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="PeptideValidationPurpose/DefaultRelaxedScoreThreshold" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="20">20</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DefaultFalseDiscoveryRateCalculator" FriendlyName="Default FDR Calculator" Category="Decoy Database Search" IsAdvanced="True" IntendedPurpose="PeptideValidation" PurposeDetails="PeptideValidationPurpose/DefaultFDRCalculator" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="ECD78FF9-3CF5-4AF6-A7D1-250925C55BA7">ECD78FF9-3CF5-4AF6-A7D1-250925C55BA7</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="ProteinScoreGuid" FriendlyName="Default Protein Score" Category="Protein Scoring" IsAdvanced="True" IntendedPurpose="ProteinValidation" PurposeDetails="ProteinValidationPurpose/DefaultProteinScore" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="E6E22773-E9A6-4a26-9694-1CA77A797099">E6E22773-E9A6-4a26-9694-1CA77A797099</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="FileSize" FriendlyName="Max. MGF File Size [MB]" Category="1. Mascot Server" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="800">800</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="SubsequentSearchSubmitTimeInterval" FriendlyName="Time interval between attempts to submit a search [sec]" Category="1. Mascot Server" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="3600">3600</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="NumberOfSubmitAttemps" FriendlyName="Number of attempts" Category="1. Mascot Server" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1000">1000</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Username" FriendlyName="Mascot User Name" Category="2. Mascot Server Authentication" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="True" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Password" FriendlyName="Mascot Server Password" Category="2. Mascot Server Authentication" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="True" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UsernameWebServer" FriendlyName="User Name" Category="3. Web Server Authentication" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="True" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="PasswordWebServer" FriendlyName="Password" Category="3. Web Server Authentication" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="True" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="MascotServerUrl" FriendlyName="Mascot Server URL" Category="1. Mascot Server" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="http://tol-brandir/mascot/">http://tol-brandir/mascot/</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="FastaDatabase" FriendlyName="Please Don't Touch this" Category="1. Input Data" IsAdvanced="True" IntendedPurpose="SequenceDatabase" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="0">0</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Database" FriendlyName="Protein Database" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="SequenceDatabaseName" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Benchmark_proteobenchFASTAModule2_DDA">Benchmark_proteobenchFASTAModule2_DDA</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Enzyme" FriendlyName="Enzyme Name" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Trypsin/P">Trypsin/P</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="EnzymeInSearch" FriendlyName="Enzyme Name" Category="1. Input Data" IsAdvanced="True" IntendedPurpose="CleavageReagent" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="Trypsin (Full)">&lt;Enzyme Version=&quot;1&quot; Name=&quot;Trypsin&quot; CleavageSites=&quot;KR&quot; CleavageInhibitors=&quot;P&quot; Offset=&quot;1&quot; CleavageSpecificity=&quot;SpecificAtBothEnds&quot; /&gt;</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="MissedCleavages" FriendlyName="Maximum Missed Cleavage Sites" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="MaximumMissedCleavages" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="2">2</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Taxonomy" FriendlyName="Taxonomy" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="All entries">All entries</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="ErrorTolerantSearch" FriendlyName="Error Tolerant Search" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="ErrorTolerantSearch" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UserEmail" FriendlyName="User email" Category="1. Input Data" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="PeptideTolerance" FriendlyName="Precursor Mass Tolerance" Category="2. Tolerances" IsAdvanced="False" IntendedPurpose="PrecursorMassTolerance" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="10 ppm">10 ppm</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="UseAveragePrecursorMass" FriendlyName="Use Average Precursor Mass" Category="2. Tolerances" IsAdvanced="False" IntendedPurpose="PrecursorAverageMassToggle" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="MascotQuanMethodName" FriendlyName="From Quan Method" Category="3. Modification Groups" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="ShowAllModifications" FriendlyName="Show All Modifications" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_1" FriendlyName="1. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Oxidation (M)">Oxidation (M)</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_2" FriendlyName="2. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Acetyl (Protein N-term)">Acetyl (Protein N-term)</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_3" FriendlyName="3. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_4" FriendlyName="4. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_5" FriendlyName="5. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_6" FriendlyName="6. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_7" FriendlyName="7. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_8" FriendlyName="8. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynMod_9" FriendlyName="9. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_1" FriendlyName="1. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_2" FriendlyName="2. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_3" FriendlyName="3. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_4" FriendlyName="4. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_5" FriendlyName="5. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_6" FriendlyName="6. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_7" FriendlyName="7. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_8" FriendlyName="8. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_9" FriendlyName="9. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_10" FriendlyName="10. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_11" FriendlyName="11. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_12" FriendlyName="12. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynModification_13" FriendlyName="13. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_1" FriendlyName="1. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_2" FriendlyName="2. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_3" FriendlyName="3. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_4" FriendlyName="4. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_5" FriendlyName="5. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_6" FriendlyName="6. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_7" FriendlyName="7. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_8" FriendlyName="8. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynTerminalModification_9" FriendlyName="9. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticMod_1" FriendlyName="1. Static Modification" Category="5. Static Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Carbamidomethyl (C)">Carbamidomethyl (C)</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticMod_2" FriendlyName="2. Static Modification" Category="5. Static Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticMod_3" FriendlyName="3. Static Modification" Category="5. Static Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticMod_4" FriendlyName="4. Static Modification" Category="5. Static Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticMod_5" FriendlyName="5. Static Modification" Category="5. Static Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticMod_6" FriendlyName="6. Static Modification" Category="5. Static Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue=""></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_1" FriendlyName="1. Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_2" FriendlyName="2. Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_3" FriendlyName="3. Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_4" FriendlyName="4. Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_5" FriendlyName="5. Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_6" FriendlyName="6. Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
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				<ProcessingNodeParameter Name="Static_Terminal2" FriendlyName="2.Static Terminal Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_Terminal3" FriendlyName="3. Static Terminal Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_Terminal4" FriendlyName="4. Static Terminal Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="Static_X" FriendlyName="X Static Modification" Category="5. Static Modifications" IsAdvanced="True" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DecoySearch" FriendlyName="Search Against Decoy Database" Category="Decoy Database Search" IsAdvanced="False" IntendedPurpose="PeptideValidation" PurposeDetails="PeptideValidationPurpose/PerformDecoySearch" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="ConcatenatedFdrCalculation" FriendlyName="ConcatenatedFdrCalculation" Category="Decoy Database Search" IsAdvanced="False" IntendedPurpose="PeptideValidation" PurposeDetails="PeptideValidationPurpose/ConcatenatedCalculation" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
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								<DataTypeAttribute>http://thermo.magellan.com/owl/DataTypes/ScoredWithNativeScore</DataTypeAttribute>
								<DataTypeAttribute>http://thermo.magellan.com/owl/DataTypes/WithDecoys</DataTypeAttribute>
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				<ProcessingNodeParameter Name="Enzyme" FriendlyName="Enzyme Name" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="CleavageReagent" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Trypsin/P (Full)">&lt;Enzyme Version=&quot;1&quot; Name=&quot;Trypsin/P&quot; CleavageSites=&quot;KR&quot; CleavageInhibitors=&quot;-&quot; Offset=&quot;1&quot; CleavageSpecificity=&quot;SpecificAtBothEnds&quot; /&gt;</ProcessingNodeParameter>
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				<ProcessingNodeParameter Name="MaximumPeptideLength" FriendlyName="Max. Peptide Length" Category="1. Input Data" IsAdvanced="False" IntendedPurpose="MaxPeptideLength" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="150">150</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="MaxPeptidesReported" FriendlyName="Max. Number of Peptides Reported" Category="1. Input Data" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="10">10</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="PeptideTolerance" FriendlyName="Precursor Mass Tolerance" Category="2. Tolerances" IsAdvanced="False" IntendedPurpose="PrecursorMassTolerance" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="10 ppm">10 ppm</ProcessingNodeParameter>
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				<ProcessingNodeParameter Name="IonSerieC" FriendlyName="Weight of c Ions" Category="3. Spectrum Matching" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesRelativeAmount" PurposeDetails="IonSeriesPurpose/C_Ions" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="0">0</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieX" FriendlyName="Weight of x Ions" Category="3. Spectrum Matching" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesRelativeAmount" PurposeDetails="IonSeriesPurpose/X_Ions" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="0">0</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieY" FriendlyName="Weight of y Ions" Category="3. Spectrum Matching" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesRelativeAmount" PurposeDetails="IonSeriesPurpose/Y_Ions" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="1">1</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="IonSerieZ" FriendlyName="Weight of z Ions" Category="3. Spectrum Matching" IsAdvanced="False" IntendedPurpose="FragmentIonSeriesRelativeAmount" PurposeDetails="IonSeriesPurpose/Z_Ions" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="0">0</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="MaxEqualModificationsPerPeptide" FriendlyName="Max. Equal Modifications Per Peptide" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="3">3</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="MaxDifferentialModificationsPerPeptide" FriendlyName="Max. Dynamic Modifications Per Peptide" Category="4. Dynamic Modifications" IsAdvanced="True" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="4">4</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModification1" FriendlyName="1. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Oxidation / +15.995 Da (M)">&lt;Modification Version=&quot;2&quot; AminoAcids=&quot;M&quot; Name=&quot;Oxidation&quot; Abbreviation=&quot;Oxidation&quot; ID=&quot;46&quot; UnimodAccession=&quot;35&quot; DeltaMass=&quot;15.99492&quot; DeltaAverageMass=&quot;15.99940&quot; IsSubstitution=&quot;False&quot; LeavingGroup=&quot;&quot; Substitution=&quot;O&quot; PositionType=&quot;Any&quot; /&gt;</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModification2" FriendlyName="2. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModification3" FriendlyName="3. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModification4" FriendlyName="4. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModification5" FriendlyName="5. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModification6" FriendlyName="6. Dynamic Modification" Category="4. Dynamic Modifications" IsAdvanced="False" IntendedPurpose="DynamicModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationNPeptide" FriendlyName="1. N-Terminal Modification" Category="5. Dynamic Modifications (peptide terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationNPeptide2" FriendlyName="2. N-Terminal Modification" Category="5. Dynamic Modifications (peptide terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationNPeptide3" FriendlyName="3. N-Terminal Modification" Category="5. Dynamic Modifications (peptide terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationCPeptide" FriendlyName="1. C-Terminal Modification" Category="5. Dynamic Modifications (peptide terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationCPeptide2" FriendlyName="2. C-Terminal Modification" Category="5. Dynamic Modifications (peptide terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationCPeptide3" FriendlyName="3. C-Terminal Modification" Category="5. Dynamic Modifications (peptide terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationNProtein" FriendlyName="1. N-Terminal Modification" Category="6. Dynamic Modifications (protein terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Acetyl / +42.011 Da (N-Terminus)">&lt;Modification Version=&quot;2&quot; AminoAcids=&quot;N-Terminus&quot; Name=&quot;Acetyl&quot; Abbreviation=&quot;Acetyl&quot; ID=&quot;2&quot; UnimodAccession=&quot;1&quot; DeltaMass=&quot;42.01057&quot; DeltaAverageMass=&quot;42.03670&quot; IsSubstitution=&quot;False&quot; LeavingGroup=&quot;&quot; Substitution=&quot;H(2) C(2) O&quot; PositionType=&quot;Protein_N_Terminus&quot; /&gt;</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationNProtein2" FriendlyName="2. N-Terminal Modification" Category="6. Dynamic Modifications (protein terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationNProtein3" FriendlyName="3. N-Terminal Modification" Category="6. Dynamic Modifications (protein terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationCProtein" FriendlyName="1. C-Terminal Modification" Category="6. Dynamic Modifications (protein terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationCProtein2" FriendlyName="2. C-Terminal Modification" Category="6. Dynamic Modifications (protein terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DynamicModificationCProtein3" FriendlyName="3. C-Terminal Modification" Category="6. Dynamic Modifications (protein terminus)" IsAdvanced="False" IntendedPurpose="DynamicTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModificationNPeptide" FriendlyName="Peptide N-Terminus" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModificationCPeptide" FriendlyName="Peptide C-Terminus" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticTerminalModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModification1" FriendlyName="1. Static Modification" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="True" IsHidden="False" IsConfig="False" DisplayValue="Carbamidomethyl / +57.021 Da (C)">&lt;Modification Version=&quot;2&quot; AminoAcids=&quot;C&quot; Name=&quot;Carbamidomethyl&quot; Abbreviation=&quot;Carbamidomethyl&quot; ID=&quot;8&quot; UnimodAccession=&quot;4&quot; DeltaMass=&quot;57.02146&quot; DeltaAverageMass=&quot;57.05130&quot; IsSubstitution=&quot;False&quot; LeavingGroup=&quot;&quot; Substitution=&quot;H(3) C(2) N O&quot; PositionType=&quot;Any&quot; /&gt;</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModification2" FriendlyName="2. Static Modification" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModification3" FriendlyName="3. Static Modification" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModification4" FriendlyName="4. Static Modification" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModification5" FriendlyName="5. Static Modification" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticModification6" FriendlyName="6. Static Modification" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="False" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="StaticJ" FriendlyName="Static Modification for J" Category="7. Static Modifications" IsAdvanced="False" IntendedPurpose="StaticModification" PurposeDetails="" IsValueSet="False" IsHidden="True" IsConfig="False" DisplayValue="None"></ProcessingNodeParameter>
				<ProcessingNodeParameter Name="AutomaticWorkLoad" FriendlyName="Automatic" Category="1. Workload Level" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="True">True</ProcessingNodeParameter>
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				<ProcessingNodeParameter Name="NumberOfParallelTasks" FriendlyName="Number of Parallel Tasks" Category="1. Workload Level" IsAdvanced="False" IntendedPurpose="Unknown" PurposeDetails="" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0">0</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge1High" FriendlyName="z=1: High Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge1LowResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1.5">1.5</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge1Middle" FriendlyName="z=1: Medium Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge1LowResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0.7">0.7</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge2High" FriendlyName="z=2: High Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge2LowResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="2">2</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge2Middle" FriendlyName="z=2: Medium Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge2LowResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0.9">0.9</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge3High" FriendlyName="z=3: High Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge3LowResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="2.5">2.5</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge3Middle" FriendlyName="z=3: Medium Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge3LowResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1.2">1.2</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge4High" FriendlyName="z&gt;=4: High Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge4LowResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="3">3</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffStdCharge4Middle" FriendlyName="z&gt;=4: Medium Confidence XCorr" Category="2. XCorr Confidence Thresholds (low-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge4LowResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1.5">1.5</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge1High" FriendlyName="z=1: High Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge1HighResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1.2">1.2</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge1Middle" FriendlyName="z=1: Medium Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge1HighResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0.7">0.7</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge2High" FriendlyName="z=2: High Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge2HighResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1.9">1.9</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge2Middle" FriendlyName="z=2: Medium Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge2HighResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="0.8">0.8</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge3High" FriendlyName="z=3: High Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge3HighResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="2.3">2.3</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge3Middle" FriendlyName="z=3: Medium Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge3HighResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1">1</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge4High" FriendlyName="z&gt;=4: High Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge4HighResolutionStrict" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="2.6">2.6</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="CutOffFTCharge4Middle" FriendlyName="z&gt;=4: Medium Confidence XCorr" Category="3. XCorr Confidence Thresholds (high-resolution data)" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/MinScoreAtCharge4HighResolutionRelaxed" IsValueSet="True" IsHidden="True" IsConfig="True" DisplayValue="1.2">1.2</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="LowResolutionSpectraContained" FriendlyName="Low resolution spectra contained" Category="3. XCorr Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="SequestPurposeDetails/LowResolutionSpectraContained" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DefaultStrictScoreThreshold" FriendlyName="Strict Score Threshold" Category="4. Default Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="PeptideValidationPurpose/DefaultStrictScoreThreshold" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="2.3">2.3</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DefaultRelaxedScoreThreshold" FriendlyName="Relaxed Score Threshold" Category="4. Default Confidence Thresholds" IsAdvanced="False" IntendedPurpose="DefaultFDRCalculatorParameter" PurposeDetails="PeptideValidationPurpose/DefaultRelaxedScoreThreshold" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="1.5">1.5</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DefaultFalseDiscoveryRateCalculator" FriendlyName="Default FDR Calculator" Category="Decoy Database Search" IsAdvanced="False" IntendedPurpose="PeptideValidation" PurposeDetails="PeptideValidationPurpose/DefaultFDRCalculator" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903">2EDB1DFD-FA0F-49B5-B8F4-EEF90C922903</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="ProteinScoreGuid" FriendlyName="Default Protein Score" Category="Protein Scoring" IsAdvanced="True" IntendedPurpose="ProteinValidation" PurposeDetails="ProteinValidationPurpose/DefaultProteinScore" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="39EFA907-9435-46E1-9AF8-1203D547387A">39EFA907-9435-46E1-9AF8-1203D547387A</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="DecoySearch" FriendlyName="Search Against Decoy Database" Category="Decoy Database Search" IsAdvanced="False" IntendedPurpose="PeptideValidation" PurposeDetails="PeptideValidationPurpose/PerformDecoySearch" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="True">True</ProcessingNodeParameter>
				<ProcessingNodeParameter Name="ConcatenatedFdrCalculation" FriendlyName="ConcatenatedFdrCalculation" Category="Decoy Database Search" IsAdvanced="False" IntendedPurpose="PeptideValidation" PurposeDetails="PeptideValidationPurpose/ConcatenatedCalculation" IsValueSet="True" IsHidden="True" IsConfig="False" DisplayValue="False">False</ProcessingNodeParameter>
			</ProcessingNodeParameters>
			<ProcessingNodePosition X="123.5" Y="253.312286376953" />
		</WorkflowNode>

We would have to specifically look for search engines?

Another question for you: we discussed using the file _StudyInformation.txt to map column headers to raw files when loading peptidoform quantities. Is it what you did? I don't see how to upload two files.

@RobbinBouwmeester
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For parameters we used to have the option to upload two files, but we might have even removed that. I know there were also some issue with regards to some formats (with regards to protein names) to get things parsed correctly. @rodvrees added a notebook that parses the input files so we can process them in proteobench.

@mlocardpaulet
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Great! Thanks. So for now, we can parse the input files ourselves with @rodvrees's notebooks.
I guess that it will give us something to then show and discuss with the developers of PD? Maybe we can see with them if there is something we miss / a way to get everything in one file?

@rodvrees
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If I'm thinking about the same thing as @RobbinBouwmeester, that notebook is specifically for MSAID data, where protein info and precursor info have to be mapped across different files. What specifically needs to happen in this case? I've never worked with PD output so if you have an example I can extend/generalize the notebook.

@mlocardpaulet
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mlocardpaulet commented Jan 15, 2025 •
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It is "just" that the column names are not understandable directly (and I did not find any safe way to make them understandable) when we want to match columns to samples.
We would need to get a second output from PD with the matching "sample" <-> "column header".
This is low priority for now (unless you disagree), specially because parameter files will also be a challenge to parse.
But we can discuss this at one point (and maybe also contact PD developers).

@rodvrees
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Okay so that's indeed very comparable to the problem we had with MSAID, I can generalize that notebook further then. Can you perhaps send me the data?

@mlocardpaulet
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The data is in the cloud (I sent you the link). There are 4 files:
image

..._PeptideGroups.txt is the quantification output
..._StudyInformation.txt is the mapping table with the name of the raw files and the name that PD gives is (F+number).

Let me know if you have any question. Thanks a lot.

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