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CHANGELOG_PARAMS
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Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AssayGeneratorMetabo + ambiguity_resolution_mz_tolerance double 10.0
AssayGeneratorMetabo + ambiguity_resolution_mz_tolerance_unit string ppm ppm,Da
AssayGeneratorMetabo + ambiguity_resolution_rt_tolerance double 10.0
AssayGeneratorMetabo + consensus_spectrum_precursor_rt_tolerance double 5.0
AssayGeneratorMetabo + decoy_generation bool false
AssayGeneratorMetabo + decoy_generation_method string original original,resolve_overlap,add_shift,both
AssayGeneratorMetabo + fingerid:candidates int 10 1:
AssayGeneratorMetabo + fingerid:db string BIO
AssayGeneratorMetabo + fragment_annotation_score_threshold double 0.8 0.0:1.0
AssayGeneratorMetabo + max_transitions int 6
AssayGeneratorMetabo + preprocessing:precursor_mz_tolerance double 10.0
AssayGeneratorMetabo + preprocessing:precursor_mz_tolerance_unit string ppm Da,ppm
AssayGeneratorMetabo + preprocessing:precursor_rt_tolerance double 5.0
AssayGeneratorMetabo + project:ignore_formula bool false
AssayGeneratorMetabo + project:processors int 1
AssayGeneratorMetabo + project:q bool false
AssayGeneratorMetabo + sirius:candidates_per_ion int -1
AssayGeneratorMetabo + sirius:compound_timeout int 100 0:
AssayGeneratorMetabo + sirius:db string
AssayGeneratorMetabo + sirius:elements_considered string
AssayGeneratorMetabo + sirius:elements_enforced string
AssayGeneratorMetabo + sirius:formula string
AssayGeneratorMetabo + sirius:ions_considered string
AssayGeneratorMetabo + sirius:ions_enforced string
AssayGeneratorMetabo + sirius:no_isotope_filter bool false
AssayGeneratorMetabo + sirius:no_isotope_score bool false
AssayGeneratorMetabo + sirius:ppm_max double 10.0
AssayGeneratorMetabo + sirius:ppm_max_ms2 double 10.0
AssayGeneratorMetabo + sirius:profile string qtof default,qtof,orbitrap,fticr
AssayGeneratorMetabo + total_occurrence_filter double 0.1 0.0:1.0
AssayGeneratorMetabo - max_transitions int 3
AssayGeneratorMetabo - precursor_rt_tolerance double 5.0
AssayGeneratorMetabo - preprocessing:precursor_mz_tolerance double 5.0e-03
AssayGeneratorMetabo - preprocessing:precursor_mz_tolerance_unit string Da Da,ppm
AssayGeneratorMetabo - preprocessing:precursor_rt_tolerance int 5
AssayGeneratorMetabo - sirius:auto_charge bool false
AssayGeneratorMetabo - sirius:compound_timeout int 10 0:
AssayGeneratorMetabo - sirius:cores int 1 1:
AssayGeneratorMetabo - sirius:database string all all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda
AssayGeneratorMetabo - sirius:elements string CHNOP[5]S[8]Cl[1]
AssayGeneratorMetabo - sirius:ion_tree bool false
AssayGeneratorMetabo - sirius:isotope string both score,filter,both,omit
AssayGeneratorMetabo - sirius:most_intense_ms2 bool false
AssayGeneratorMetabo - sirius:noise int 0 0:
AssayGeneratorMetabo - sirius:ppm_max int 10
AssayGeneratorMetabo - sirius:profile string qtof qtof,orbitrap,fticr
AssayGeneratorMetabo - sirius:top_n_hits int 10 1:
CometAdapter + enzyme string Trypsin Trypsin,Chymotrypsin,Lys-C,Lys-N,Asp-N,CNBr,PepsinA,unspecific cleavage,Trypsin/P,glutamyl endopeptidase,Arg-C
CometAdapter + second_enzyme string Trypsin,Chymotrypsin,Lys-C,Lys-N,Asp-N,CNBr,PepsinA,unspecific cleavage,Trypsin/P,glutamyl endopeptidase,Arg-C
CometAdapter - enzyme string Trypsin Arg-C,Trypsin,Asp-N,glutamyl endopeptidase,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
CometAdapter - second_enzyme string Arg-C,Trypsin,Asp-N,glutamyl endopeptidase,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
ConsensusID + PEPMatrix:matrix string PAM30MS identity,PAM30MS
ConsensusID - PEPMatrix:matrix string identity identity,PAM30MS
CruxAdapter + enzyme string trypsin custom-enzyme,asp-n,chymotrypsin,arg-c,iodosobenzoate,staph-protease,proline-endopeptidase,glu-c,no-enzyme,lys-c,lys-n,trypsin/p,elastase,pepsin-a,cyanogen-bromide,clostripain,elastase-trypsin-chymotrypsin,trypsin
CruxAdapter - enzyme string trypsin custom-enzyme,no-enzyme,trypsin,elastase,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,elastase-trypsin-chymotrypsin,arg-c,asp-n,chymotrypsin,lys-c,lys-n,trypsin/p,iodosobenzoate,staph-protease
DecoyDatabase + enzyme string Trypsin Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Asp-N/B,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,no cleavage,unspecific cleavage,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin
DecoyDatabase - enzyme string Trypsin Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,V8-DE,V8-E,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
Digestor + enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin
Digestor - enzyme string Trypsin Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DigestorMotif + enzyme string Trypsin 2-iodobenzoate,iodosobenzoate,Arg-C/P,Asp-N,Asp-N/B,Arg-C,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Trypsin
DigestorMotif - enzyme string Trypsin cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P
FeatureFinderIdentification + EMGScoring:init_mom bool false
FeatureFinderIdentification + EMGScoring:max_iteration int 100 1:
FeatureFinderIdentification + extract:batch_size int 5000 1:
FeatureFinderIdentification + quantify_decoys bool false
FeatureFinderIdentification + svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderIdentification - extract:batch_size int 1000 1:
FeatureFinderIdentification - svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderMetaboIdent + EMGScoring:init_mom bool false
FeatureFinderMetaboIdent + EMGScoring:max_iteration int 100 1:
FeatureFinderMetaboIdent + debug int 0 0:
FeatureFinderMetaboIdent + detect:peak_width double 60.0 0.0:
FeatureFinderMetaboIdent - debug int 0
FeatureFinderMetaboIdent - detect:peak_width double 5.0 0.0:
FeatureLinkerUnlabeledQT + algorithm:min_IDscore_forTolCalc double 1.0
FeatureLinkerUnlabeledQT + algorithm:min_nr_diffs_per_bin int 50 5:
FeatureLinkerUnlabeledQT + algorithm:noID_penalty double 0.0 0.0:1.0
FileConverter + change_im_format string none none,concatenated,multiple_spectra,mixed
FileConverter + out output-file *.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv,*.sqmass
FileConverter + out_type string mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv,sqmass
FileConverter - change_im_format string none none,multiple,single
FileConverter - out output-file *.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv
FileConverter - out_type string mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.sqMass,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo + in_type string mzData,mzXML,mzML,sqMass,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp
GNPSExport + merged_spectra:cos_similarity double 0.9 0.0:
GNPSExport + merged_spectra:precursor_mass_tolerance double 0.5 0.0:
GNPSExport + ms2_bin_size double 0.019999999552965 0.0:
GNPSExport + output_type string most_intense merged_spectra,most_intense
GNPSExport + peptide_cutoff int 5 -1:
GNPSExport - merged_spectra:cos_similarity double 0.95
GNPSExport - output_type string full_spectra full_spectra,merged_spectra
GNPSExport - precursor_mz_tolerance double 1.0e-04
GNPSExport - precursor_rt_tolerance double 5.0
IDFileConverter + fasta_to_mzml:a_intensity double 1.0
IDFileConverter + fasta_to_mzml:add_a_ions bool false
IDFileConverter + fasta_to_mzml:add_abundant_immonium_ions bool false
IDFileConverter + fasta_to_mzml:add_all_precursor_charges bool false
IDFileConverter + fasta_to_mzml:add_b_ions string true true,false
IDFileConverter + fasta_to_mzml:add_c_ions bool false
IDFileConverter + fasta_to_mzml:add_first_prefix_ion bool false
IDFileConverter + fasta_to_mzml:add_losses bool false
IDFileConverter + fasta_to_mzml:add_metainfo bool false
IDFileConverter + fasta_to_mzml:add_precursor_peaks bool false
IDFileConverter + fasta_to_mzml:add_x_ions bool false
IDFileConverter + fasta_to_mzml:add_y_ions string true true,false
IDFileConverter + fasta_to_mzml:add_z_ions bool false
IDFileConverter + fasta_to_mzml:b_intensity double 1.0
IDFileConverter + fasta_to_mzml:c_intensity double 1.0
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Arg-C,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,no cleavage,unspecific cleavage,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin
IDFileConverter + fasta_to_mzml:isotope_model string none none,coarse,fine
IDFileConverter + fasta_to_mzml:max_charge int 1
IDFileConverter + fasta_to_mzml:max_isotope int 2
IDFileConverter + fasta_to_mzml:max_isotope_probability double 0.05
IDFileConverter + fasta_to_mzml:min_charge int 1
IDFileConverter + fasta_to_mzml:missed_cleavages int 0
IDFileConverter + fasta_to_mzml:precursor_H2O_intensity double 1.0
IDFileConverter + fasta_to_mzml:precursor_NH3_intensity double 1.0
IDFileConverter + fasta_to_mzml:precursor_charge int 0
IDFileConverter + fasta_to_mzml:precursor_intensity double 1.0
IDFileConverter + fasta_to_mzml:relative_loss_intensity double 0.1
IDFileConverter + fasta_to_mzml:sort_by_position string true true,false
IDFileConverter + fasta_to_mzml:x_intensity double 1.0
IDFileConverter + fasta_to_mzml:y_intensity double 1.0
IDFileConverter + fasta_to_mzml:z_intensity double 1.0
IDFileConverter + in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml,*.fasta
IDFileConverter + out output-file *.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml,*.mzML
IDFileConverter + out_type string idXML,mzid,pepXML,FASTA,xquest.xml,mzML
IDFileConverter - in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml
IDFileConverter - out output-file *.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml
IDFileConverter - out_type string idXML,mzid,pepXML,FASTA,xquest.xml
IDFilter + best:n_spectra int 0 0:
IDFilter + blacklist:RegEx string
IDFilter + in_silico_digestion:enzyme string Trypsin Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,no cleavage,unspecific cleavage,Arg-C/P,PepsinA,TrypChymo,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-E,leukocyte elastase,proline endopeptidase,Trypsin/P,V8-DE,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B
IDFilter + missed_cleavages:enzyme string Trypsin Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,no cleavage,unspecific cleavage,Arg-C/P,PepsinA,TrypChymo,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-E,leukocyte elastase,proline endopeptidase,Trypsin/P,V8-DE,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B
IDFilter - in_silico_digestion:enzyme string Trypsin Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N_ambic,Chymotrypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
IDFilter - missed_cleavages:enzyme string Trypsin Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N_ambic,Chymotrypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
MSFraggerAdapter + digest:search_enzyme_name string Trypsin PepsinA,TrypChymo,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Lys-N,Lys-C/P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Formic_acid,Lys-C,Arg-C,Arg-C/P,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,no cleavage,unspecific cleavage,Trypsin
MSFraggerAdapter + license string yes,no
MSFraggerAdapter + search:localize_delta_mass int 0 0:
MSFraggerAdapter + tolerance:precursor_mass_tolerance_lower double 20.0 0.0:
MSFraggerAdapter + tolerance:precursor_mass_tolerance_upper double 20.0 0.0:
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
MSFraggerAdapter - tolerance:precursor_mass_tolerance double 20.0 0.0:
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Trypsin
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Trypsin,Arg-C,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,V8-DE,V8-E,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
MascotAdapterOnline + Mascot_parameters:decoy bool false
MascotAdapterOnline + Mascot_server:batch_size int 50000 0:
MascotAdapterOnline - keep_protein_links bool false
MzTabExporter + export_all_psms bool false
NucleicAcidSearchEngine + oligo:enzyme string no cleavage RNase_T1,cusativin,RNase_H,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_U2,RNase_A,RNase_MC1
NucleicAcidSearchEngine - oligo:enzyme string no cleavage RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,no cleavage,unspecific cleavage
OMSSAAdapter + enzyme string Trypsin Trypsin,glutamyl endopeptidase,Lys-C/P,no cleavage,unspecific cleavage,CNBr,Formic_acid,Lys-C,Asp-N_ambic,Chymotrypsin,Asp-N,PepsinA,TrypChymo,Trypsin/P,Arg-C
OMSSAAdapter - enzyme string Trypsin Trypsin,CNBr,Formic_acid,Asp-N_ambic,Chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Asp-N,Lys-C,Lys-C/P,Arg-C,PepsinA,TrypChymo,Trypsin/P
OpenPepXL + algorithm:number_top_hits int 1
OpenPepXL + fragment:mass_tolerance double 20.0
OpenPepXL + fragment:mass_tolerance_unit string ppm ppm,Da
OpenPepXL + fragment:mass_tolerance_xlinks double 20.0
OpenPepXL + modifications:variable_max_per_peptide int 3
OpenPepXL + peptide:enzyme string Trypsin Trypsin,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C/P,PepsinA,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,TrypChymo,Trypsin/P,V8-DE,V8-E,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr
OpenPepXL + peptide:missed_cleavages int 3
OpenPepXL + precursor:max_charge int 8
OpenPepXL + precursor:min_charge int 2
OpenPepXL - algorithm:number_top_hits int 5
OpenPepXL - fragment:mass_tolerance double 0.2
OpenPepXL - fragment:mass_tolerance_unit string Da ppm,Da
OpenPepXL - fragment:mass_tolerance_xlinks double 0.3
OpenPepXL - modifications:variable_max_per_peptide int 2
OpenPepXL - peptide:enzyme string Trypsin Trypsin,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic
OpenPepXL - peptide:missed_cleavages int 2
OpenPepXL - precursor:max_charge int 7
OpenPepXL - precursor:min_charge int 3
OpenPepXLLF + algorithm:number_top_hits int 1
OpenPepXLLF + modifications:variable_max_per_peptide int 3
OpenPepXLLF + peptide:enzyme string Trypsin Trypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage,Arg-C,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin
OpenPepXLLF + peptide:missed_cleavages int 3
OpenPepXLLF + precursor:max_charge int 8
OpenPepXLLF + precursor:min_charge int 2
OpenPepXLLF - algorithm:number_top_hits int 5
OpenPepXLLF - modifications:variable_max_per_peptide int 2
OpenPepXLLF - peptide:enzyme string Trypsin Trypsin,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic
OpenPepXLLF - peptide:missed_cleavages int 2
OpenPepXLLF - precursor:max_charge int 7
OpenPepXLLF - precursor:min_charge int 3
OpenSwathAnalyzer + algorithm:EMGScoring:init_mom bool false
OpenSwathAnalyzer + algorithm:Scores:use_ionseries_scores string true true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms2_isotope_scores string true true,false
OpenSwathRTNormalizer + algorithm:EMGScoring:init_mom bool false
OpenSwathRTNormalizer + algorithm:Scores:use_ionseries_scores string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms2_isotope_scores string true true,false
OpenSwathWorkflow + Scoring:EMGScoring:init_mom bool false
OpenSwathWorkflow + Scoring:Scores:use_ionseries_scores string true true,false
OpenSwathWorkflow + Scoring:Scores:use_ms2_isotope_scores string true true,false
PeptideIndexer + enzyme:name string auto auto,Lys-N,Lys-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C,Arg-C/P,Asp-N,Formic_acid,Lys-C,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,PepsinA,TrypChymo,Trypsin/P,V8-DE,Trypsin
PeptideIndexer - enzyme:name string auto auto,Asp-N,Asp-N/B,Asp-N_ambic,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid
PercolatorAdapter + osw_level string ms2 ms1,ms2,transition
PercolatorAdapter - osw_level string ms2
ProteomicsLFQ + Alignment:align_algorithm:max_rt_shift double 0.1 0.0:
ProteomicsLFQ + Alignment:align_algorithm:min_run_occur int 2 2:
ProteomicsLFQ + Alignment:align_algorithm:min_score double 0.05
ProteomicsLFQ + Alignment:align_algorithm:score_cutoff bool false
ProteomicsLFQ + Alignment:align_algorithm:use_feature_rt string true true,false
ProteomicsLFQ + Alignment:align_algorithm:use_unassigned_peptides bool false
ProteomicsLFQ + Alignment:model:b_spline:boundary_condition int 2 0:2
ProteomicsLFQ + Alignment:model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
ProteomicsLFQ + Alignment:model:b_spline:num_nodes int 5 0:
ProteomicsLFQ + Alignment:model:b_spline:wavelength double 0.0 0.0:
ProteomicsLFQ + Alignment:model:interpolated:extrapolation_type string two-point-linear two-point-linear,four-point-linear,global-linear
ProteomicsLFQ + Alignment:model:interpolated:interpolation_type string cspline linear,cspline,akima
ProteomicsLFQ + Alignment:model:linear:symmetric_regression bool false
ProteomicsLFQ + Alignment:model:linear:x_datum_max double 1.0e15
ProteomicsLFQ + Alignment:model:linear:x_datum_min double 1.0e-15
ProteomicsLFQ + Alignment:model:linear:x_weight string 1/x,1/x2,ln(x),
ProteomicsLFQ + Alignment:model:linear:y_datum_max double 1.0e15
ProteomicsLFQ + Alignment:model:linear:y_datum_min double 1.0e-15
ProteomicsLFQ + Alignment:model:linear:y_weight string 1/y,1/y2,ln(y),
ProteomicsLFQ + Alignment:model:lowess:delta double -1.0
ProteomicsLFQ + Alignment:model:lowess:extrapolation_type string four-point-linear two-point-linear,four-point-linear,global-linear
ProteomicsLFQ + Alignment:model:lowess:interpolation_type string cspline linear,cspline,akima
ProteomicsLFQ + Alignment:model:lowess:num_iterations int 3 0:
ProteomicsLFQ + Alignment:model:lowess:span double 0.666666666666667 0.0:1.0
ProteomicsLFQ + Alignment:model:type string b_spline linear,b_spline,lowess,interpolated
ProteomicsLFQ + Alignment:model_type string b_spline linear,b_spline,lowess,interpolated
ProteomicsLFQ + Linking:min_IDscore_forTolCalc double 1.0
ProteomicsLFQ + Linking:min_nr_diffs_per_bin int 50 5:
ProteomicsLFQ + Linking:noID_penalty double 0.0 0.0:1.0
ProteomicsLFQ + PeptideQuantification:EMGScoring:init_mom bool false
ProteomicsLFQ + PeptideQuantification:EMGScoring:max_iteration int 100 1:
ProteomicsLFQ + PeptideQuantification:extract:batch_size int 5000 1:
ProteomicsLFQ + PeptideQuantification:quantify_decoys bool false
ProteomicsLFQ + PeptideQuantification:svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
ProteomicsLFQ + Seeding:charge string 2:5
ProteomicsLFQ + Seeding:intThreshold double 1.0e04
ProteomicsLFQ + Seeding:traceRTTolerance double 3.0
ProteomicsLFQ + alignment_order string star star,treeguided
ProteomicsLFQ + out_triqler output-file *.tsv
ProteomicsLFQ - Alignment:max_rt_shift double 0.1 0.0:
ProteomicsLFQ - Alignment:min_run_occur int 2 2:
ProteomicsLFQ - Alignment:min_score double 0.05
ProteomicsLFQ - Alignment:score_cutoff bool false
ProteomicsLFQ - Alignment:use_feature_rt string true true,false
ProteomicsLFQ - Alignment:use_unassigned_peptides bool false
ProteomicsLFQ - PeptideQuantification:extract:batch_size int 1000 1:
ProteomicsLFQ - PeptideQuantification:svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
ProteomicsLFQ - seedThreshold double 1.0e04
QCCalculator + address string
QCCalculator + description string
QCCalculator + label string label
QCCalculator + name string
QCCalculator + out output-file *.mzQC,*.qcML
QCCalculator + out_type string mzQC,qcML
QCCalculator - out output-file *.qcML
QualityControl + out_evd string
RNADigestor + enzyme string RNase_T1 RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,mazF,colicin_E5,no cleavage,unspecific cleavage
RNADigestor - enzyme string RNase_T1 RNase_T1,RNase_MC1,RNase_H,no cleavage,unspecific cleavage,cusativin,RNase_U2,RNase_A
RNPxlSearch + peptide:enzyme string Trypsin PepsinA,TrypChymo,Trypsin/P,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C/P,Lys-C,Lys-N,Lys-C/P,Arg-C,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
RNPxlSearch - peptide:enzyme string Trypsin proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,no cleavage,unspecific cleavage,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
SimpleSearchEngine + Search:annotate:PSM string ALL,fragment_mz_error_median_ppm,precursor_mz_error_ppm,matched_prefix_ions_fraction,matched_suffix_ions_fraction
SimpleSearchEngine + Search:enzyme string Trypsin Trypsin,Lys-C/P,PepsinA,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Lys-C,Lys-N,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C/P,TrypChymo,Trypsin/P
SimpleSearchEngine - Search:annotate:PSM string fragment_mz_error_median_ppm,precursor_mz_error_ppm
SimpleSearchEngine - Search:enzyme string Trypsin Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,TrypChymo,Arg-C/P,Arg-C,unspecific cleavage,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Lys-C,Lys-N,Chymotrypsin/P,CNBr,Formic_acid
SiriusAdapter + fingerid:candidates int 10 1:
SiriusAdapter + fingerid:db string BIO
SiriusAdapter + out_project_space string
SiriusAdapter + preprocessing:precursor_mz_tolerance double 10.0
SiriusAdapter + preprocessing:precursor_mz_tolerance_unit string ppm Da,ppm
SiriusAdapter + preprocessing:precursor_rt_tolerance double 5.0
SiriusAdapter + project:ignore_formula bool false
SiriusAdapter + project:processors int 1
SiriusAdapter + project:q bool false
SiriusAdapter + sirius:candidates_per_ion int -1
SiriusAdapter + sirius:compound_timeout int 100 0:
SiriusAdapter + sirius:db string
SiriusAdapter + sirius:elements_considered string
SiriusAdapter + sirius:elements_enforced string
SiriusAdapter + sirius:formula string
SiriusAdapter + sirius:ions_considered string
SiriusAdapter + sirius:ions_enforced string
SiriusAdapter + sirius:no_isotope_filter bool false
SiriusAdapter + sirius:no_isotope_score bool false
SiriusAdapter + sirius:ppm_max double 10.0
SiriusAdapter + sirius:ppm_max_ms2 double 10.0
SiriusAdapter + sirius:profile string qtof default,qtof,orbitrap,fticr
SiriusAdapter - out_workspace_directory string
SiriusAdapter - preprocessing:precursor_mz_tolerance double 5.0e-03
SiriusAdapter - preprocessing:precursor_mz_tolerance_unit string Da Da,ppm
SiriusAdapter - preprocessing:precursor_rt_tolerance int 5
SiriusAdapter - sirius:auto_charge bool false
SiriusAdapter - sirius:compound_timeout int 10 0:
SiriusAdapter - sirius:cores int 1 1:
SiriusAdapter - sirius:database string all all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda
SiriusAdapter - sirius:elements string CHNOP[5]S[8]Cl[1]
SiriusAdapter - sirius:ion_tree bool false
SiriusAdapter - sirius:isotope string both score,filter,both,omit
SiriusAdapter - sirius:most_intense_ms2 bool false
SiriusAdapter - sirius:noise int 0 0:
SiriusAdapter - sirius:ppm_max int 10
SiriusAdapter - sirius:profile string qtof qtof,orbitrap,fticr
SiriusAdapter - sirius:top_n_hits int 10 1:
SpectraMerger + algorithm:sort_blocks string RT_ascending RT_ascending,RT_descending
SpectraMerger - algorithm:sort_blocks string RT_ascending RT_ascending, RT_descending
TextExporter + out output-file *.tsv,*.csv,*.txt
TextExporter + out_type string tsv,csv,txt
TextExporter - out output-file *.tsv
TextExporter - separator string
XTandemAdapter + enzyme string Trypsin PepsinA,TrypChymo,Trypsin/P,Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,unspecific cleavage,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Lys-C,Lys-N,Lys-C/P,Arg-C,V8-DE,V8-E,leukocyte elastase
XTandemAdapter - enzyme string Trypsin Asp-N_ambic,Chymotrypsin,Trypsin,Formic_acid,Lys-C,Alpha-lytic protease,2-iodobenzoate,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Chymotrypsin/P,CNBr,Arg-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase