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CHANGELOG_PARAMS
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CHANGELOG_PARAMS
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Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + algorithm:mzTab:exportIsotopeIntensities string false false,true
AccurateMassSearch + algorithm:use_feature_adducts string false false,true
AccurateMassSearch - algorithm:mzTab:exportIsotopeIntensities int 0 0:
AssayGeneratorMetabo + deisotoping:annotate_charge string false true,false
AssayGeneratorMetabo + deisotoping:fragment_tolerance double 1.0
AssayGeneratorMetabo + deisotoping:fragment_unit string ppm ppm,Da
AssayGeneratorMetabo + deisotoping:keep_only_deisotoped string false true,false
AssayGeneratorMetabo + deisotoping:max_charge int 1 1:
AssayGeneratorMetabo + deisotoping:max_isopeaks int 3 3:
AssayGeneratorMetabo + deisotoping:min_charge int 1 1:
AssayGeneratorMetabo + deisotoping:min_isopeaks int 2 2:
AssayGeneratorMetabo + deisotoping:use_deisotoper string false true,false
AssayGeneratorMetabo + exclude_ms2_precursor string false true,false
AssayGeneratorMetabo + executable input-file
AssayGeneratorMetabo + fragment_annotation string none none,sirius
AssayGeneratorMetabo + max_transitions int 6
AssayGeneratorMetabo + min_transitions int 3
AssayGeneratorMetabo + out output-file *.tsv,*.traML,*.pqp
AssayGeneratorMetabo + out_workspace_directory string
AssayGeneratorMetabo + precursor_mz_distance double 1.0e-04
AssayGeneratorMetabo + precursor_rt_tolerance double 5.0
AssayGeneratorMetabo + preprocessing:feature_only string false true,false
AssayGeneratorMetabo + preprocessing:filter_by_num_masstraces int 1 1:
AssayGeneratorMetabo + preprocessing:isotope_pattern_iterations int 3
AssayGeneratorMetabo + preprocessing:no_masstrace_info_isotope_pattern string false true,false
AssayGeneratorMetabo + preprocessing:precursor_mz_tolerance double 0.005
AssayGeneratorMetabo + preprocessing:precursor_mz_tolerance_unit string Da Da,ppm
AssayGeneratorMetabo + preprocessing:precursor_rt_tolerance int 5
AssayGeneratorMetabo + sirius:auto_charge string false true,false
AssayGeneratorMetabo + sirius:candidates int 5 1:
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 string false true,false
AssayGeneratorMetabo + sirius:isotope string both score,filter,both,omit
AssayGeneratorMetabo + sirius:most_intense_ms2 string false true,false
AssayGeneratorMetabo + sirius:no_recalibration string false true,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:
AssayGeneratorMetabo + sirius:tree_timeout int 0 0:
AssayGeneratorMetabo + transition_threshold double 10.0
AssayGeneratorMetabo + use_exact_mass string false true,false
AssayGeneratorMetabo - filter_by_convex_hulls int 2
AssayGeneratorMetabo - out output-file *.tsv
AssayGeneratorMetabo - precursor_mz_distance double 0.0001
AssayGeneratorMetabo - precursor_mz_tolerance double 0.005
AssayGeneratorMetabo - precursor_mz_tolerance_unit string Da Da,ppm
AssayGeneratorMetabo - precursor_rt_tolerance double 5
AssayGeneratorMetabo - transition_threshold double 10
CometAdapter + enzyme string Trypsin unspecific cleavage,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,Arg-C,Trypsin
CometAdapter - enzyme string Trypsin Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage,Trypsin
CruxAdapter + enzyme string trypsin custom-enzyme,chymotrypsin,lys-c,lys-n,trypsin/p,elastase,iodosobenzoate,staph-protease,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,asp-n,trypsin,arg-c,elastase-trypsin-chymotrypsin,no-enzyme
CruxAdapter - enzyme string trypsin custom-enzyme,chymotrypsin,lys-c,lys-n,trypsin/p,elastase,arg-c,iodosobenzoate,staph-protease,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,elastase-trypsin-chymotrypsin,no-enzyme,asp-n,trypsin
DecoyDatabase + enzyme string Trypsin Asp-N,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Asp-N/B,Arg-C/P,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
DecoyDatabase + type string protein protein,RNA
DecoyDatabase - enzyme string Trypsin leukocyte elastase,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,Asp-N/B,Chymotrypsin/P,Chymotrypsin,V8-DE,V8-E,proline endopeptidase,TrypChymo,Trypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Alpha-lytic protease,glutamyl endopeptidase,Asp-N,Asp-N_ambic,Arg-C/P,Trypsin
Digestor + enzyme string Trypsin 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,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
Digestor - enzyme string Trypsin Trypsin,Arg-C/P,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,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
DigestorMotif + enzyme string Trypsin Trypsin,elastase-trypsin-chymotrypsin,no cleavage,cyanogen-bromide,Clostripain/P,Chymotrypsin,Chymotrypsin/P,CNBr,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,proline-endopeptidase/HKR,staphylococcal protease/D,Glu-C+P,PepsinA + P,unspecific cleavage,Formic_acid,Asp-N/B,Asp-N_ambic,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,proline endopeptidase,leukocyte elastase,Arg-C,Arg-C/P,Asp-N
DigestorMotif - enzyme string Trypsin Arg-C/P,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,elastase-trypsin-chymotrypsin,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,unspecific cleavage,Trypsin
FalseDiscoveryRate + FDR:cleanup:remove_proteins_without_psms string true true,false
FalseDiscoveryRate + FDR:cleanup:remove_psms_without_proteins string true true,false
FalseDiscoveryRate + FDR:cleanup:remove_spectra_without_psms string true true,false
FalseDiscoveryRate + algorithm:conservative string true true,false
FeatureFinderCentroided + algorithm:isotopic_pattern:abundance_12C double 98.930000000000007 0.0:100.0
FeatureFinderCentroided + algorithm:isotopic_pattern:abundance_14N double 99.632000000000005 0.0:100.0
FeatureFinderCentroided - algorithm:isotopic_pattern:abundance_12C double 98.93 0:100
FeatureFinderCentroided - algorithm:isotopic_pattern:abundance_14N double 99.632 0:100
FeatureFinderMetabo + algorithm:mtd:quant_method string area area,median,max_height
FeatureFinderMetabo - algorithm:mtd:quant_method string area area,median
FeatureFinderMultiplex + out_blacklist output-file *.mzML
FeatureLinkerUnlabeledKD + algorithm:link:adduct_merging string Any Identical,With_unknown_adducts,Any
FeatureLinkerUnlabeledKD + algorithm:link:charge_merging string With_charge_zero Identical,With_charge_zero,Any
FeatureLinkerUnlabeledKD - algorithm:ignore_adduct string true true,false
FileConverter + NET_executable input-file
FileConverter + ThermoRaw_executable input-file ThermoRawFileParser.exe *.exe
FileConverter + change_im_format string none none,multiple,single
FileConverter + in input-file *.mzML,*.mzXML,*.mgf,*.raw,*.cachedMzML,*.mzData,*.dta,*.dta2d,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter + in_type string mzML,mzXML,mgf,raw,cachedMzML,mzData,dta,dta2d,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
FileConverter + no_peak_picking string false true,false
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
FileConverter - in input-file *.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter - in_type string mzData,mzXML,mzML,cachedMzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
FileConverter - out output-file *.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter - out_type string mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv
FileFilter + peak_options:numpress:float_da string none none,linear,pic,slof
FileFilter + peak_options:numpress:lossy_mass_accuracy double -1.0
FileFilter + peak_options:remove_empty string false true,false
FileFilter - peak_options:numpress:intensity_error double 0.0001
FileFilter - peak_options:numpress:masstime_error double 0.0001
FileMerger + append_method string append_rows append_rows,append_cols
HighResPrecursorMassCorrector + highest_intensity_peak:mz_tolerance_unit string ppm Da,ppm
IDFileConverter + no_spectra_references_override string false true,false
IDFilter + in_silico_digestion:enzyme string Trypsin staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,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,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter + missed_cleavages:enzyme string Trypsin staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,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,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter + precursor:charge string :
IDFilter + precursor:length string :
IDFilter + remove_duplicate_psm string false true,false
IDFilter + remove_peptide_hits_by_metavalue string
IDFilter + remove_shared_peptides string false true,false
IDFilter - charge string :
IDFilter - in_silico_digestion:enzyme string Trypsin Arg-C,Asp-N/B,Asp-N,Trypsin,Arg-C/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter - length string :
IDFilter - missed_cleavages:enzyme string Trypsin Arg-C,Asp-N/B,Asp-N,Trypsin,Arg-C/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter - thresh:pep double 0
IDFilter - thresh:prot double 0
IDFilter - unique string false true,false
IDFilter - unique_per_protein string false true,false
IDMapper + feature:use_centroid_mz string true true,false
IDMapper + mz_reference string peptide precursor,peptide
IDMapper - feature:use_centroid_mz string false true,false
IDMapper - mz_reference string precursor precursor,peptide
IDMerger + merge_proteins_add_PSMs string false true,false
IDPosteriorErrorProbability + fit_algorithm:neg_log_delta int 6
ImageCreator + mz string :
ImageCreator + rt string :
InternalCalibration + goodness:MAD double 2.0
InternalCalibration - goodness:MAD double 1
IsobaricAnalyzer + tmt16plex:channel_126_description string
IsobaricAnalyzer + tmt16plex:channel_127C_description string
IsobaricAnalyzer + tmt16plex:channel_127N_description string
IsobaricAnalyzer + tmt16plex:channel_128C_description string
IsobaricAnalyzer + tmt16plex:channel_128N_description string
IsobaricAnalyzer + tmt16plex:channel_129C_description string
IsobaricAnalyzer + tmt16plex:channel_129N_description string
IsobaricAnalyzer + tmt16plex:channel_130C_description string
IsobaricAnalyzer + tmt16plex:channel_130N_description string
IsobaricAnalyzer + tmt16plex:channel_131C_description string
IsobaricAnalyzer + tmt16plex:channel_131N_description string
IsobaricAnalyzer + tmt16plex:channel_132C_description string
IsobaricAnalyzer + tmt16plex:channel_132N_description string
IsobaricAnalyzer + tmt16plex:channel_133C_description string
IsobaricAnalyzer + tmt16plex:channel_133N_description string
IsobaricAnalyzer + tmt16plex:channel_134N_description string
IsobaricAnalyzer + tmt16plex:correction_matrix string
IsobaricAnalyzer + tmt16plex:reference_channel string 126 126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C,132N,132C,133N,133C,134N
IsobaricAnalyzer + type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt6plex
IsobaricAnalyzer - type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt6plex
LuciphorAdapter + rt_tolerance double 0.01 0.0:
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:write_sn_log_messages string false true,false
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:write_sn_log_messages string true true,false
MSFraggerAdapter + digest:search_enzyme_name string Trypsin Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,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
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Trypsin,Arg-C/P,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,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
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Arg-C/P,Asp-N,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,Alpha-lytic protease,glutamyl endopeptidase,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Asp-N/B,Arg-C,Trypsin
MSstatsConverter + method string LFQ LFQ,ISO
MSstatsConverter + msstats_mixture string MSstats_Mixture
MapAlignerIdentification + algorithm:min_score double 0.05
MapAlignerIdentification + algorithm:score_cutoff string false true,false
MassTraceExtractor + algorithm:mtd:quant_method string area area,median,max_height
MassTraceExtractor - algorithm:mtd:quant_method string area area,median
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:mass_max_diff double 0.05 0.0:
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:unit string Da Da,ppm
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:mass_max_diff double 0.05
MultiplexResolver + algorithm:mz_tolerance int 10
MultiplexResolver + algorithm:rt_tolerance int 5
MultiplexResolver + in_blacklist input-file *.mzML
MzTabExporter + first_run_inference_only string false true,false
MzTabExporter + opt_columns string subfeatures
OMSSAAdapter + enzyme string Trypsin Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage
OMSSAAdapter - enzyme string Trypsin Arg-C,unspecific cleavage,Asp-N,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,Trypsin,Asp-N_ambic,Chymotrypsin,CNBr
OpenPepXL + decoy_prefix string true true,false
OpenPepXL + decoy_string string DECOY_
OpenPepXL + peptide:enzyme string Trypsin Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXL - decoy_prefix string false true,false
OpenPepXL - decoy_string string decoy
OpenPepXL - peptide:enzyme string Trypsin iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,proline endopeptidase,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,V8-DE,V8-E,leukocyte elastase,Arg-C,Arg-C/P,Trypsin
OpenPepXLLF + decoy_prefix string true true,false
OpenPepXLLF + decoy_string string DECOY_
OpenPepXLLF + peptide:enzyme string Trypsin Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,proline-endopeptidase/HKR,Arg-C/P,staphylococcal protease/D,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXLLF + algorithm:use_sequence_tags string false true,false
OpenPepXLLF + algorithm:sequence_tag_min_length int 2
OpenPepXLLF - algorithm:number_of_scored_candidates int 10000
OpenPepXLLF - algorithm:pre_scoring string false true,false
OpenPepXLLF - decoy_prefix string false true,false
OpenPepXLLF - decoy_string string decoy
OpenPepXLLF - peptide:enzyme string Trypsin Asp-N/B,Asp-N,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,Alpha-lytic protease,glutamyl endopeptidase,Trypsin,Arg-C,Arg-C/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P
OpenSwathAnalyzer + algorithm:Scores:use_ion_mobility_scores string false true,false
OpenSwathAnalyzer + algorithm:im_extra_drift double 0.0 0.0:
OpenSwathAnalyzer + algorithm:spectrum_addition_method string simple simple,resample
OpenSwathFileSplitter + out_qc output-file *.json
OpenSwathRTNormalizer + algorithm:Scores:use_ion_mobility_scores string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages string false true,false
OpenSwathRTNormalizer + algorithm:im_extra_drift double 0.0 0.0:
OpenSwathRTNormalizer + algorithm:spectrum_addition_method string simple simple,resample
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages string true true,false
OpenSwathWorkflow + Calibration:debug_im_file string
OpenSwathWorkflow + Calibration:debug_mz_file string
OpenSwathWorkflow + Calibration:im_correction_function string linear none,linear
OpenSwathWorkflow + Calibration:ms1_im_calibration string false true,false
OpenSwathWorkflow + Debugging:irt_mzml output-file *.mzML
OpenSwathWorkflow + Debugging:irt_trafo output-file *.trafoXML
OpenSwathWorkflow + Scoring:Scores:use_ion_mobility_scores string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:min_peak_width double -1.0
OpenSwathWorkflow + Scoring:add_up_spectra int 1 1:
OpenSwathWorkflow + Scoring:im_extra_drift double 0.0 0.0:
OpenSwathWorkflow + Scoring:spacing_for_spectra_resampling double 0.005 0.0:
OpenSwathWorkflow + Scoring:spectrum_addition_method string simple simple,resample
OpenSwathWorkflow + Scoring:stop_report_after_feature int 5
OpenSwathWorkflow + batchSize int 250 0:
OpenSwathWorkflow + im_extraction_window_ms1 double -1.0
OpenSwathWorkflow + irt_im_extraction_window double -1.0
OpenSwathWorkflow + irt_mz_extraction_window double 0.05 0.0:
OpenSwathWorkflow + irt_mz_extraction_window_unit string Th Th,ppm
OpenSwathWorkflow + matching_window_only string false true,false
OpenSwathWorkflow + ms1_isotopes int 0 0:
OpenSwathWorkflow + mz_correction_function string none none,regression_delta_ppm,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm
OpenSwathWorkflow + mz_extraction_window_ms1 double 0.05 0.0:
OpenSwathWorkflow + mz_extraction_window_ms1_unit string Th ppm,Th
OpenSwathWorkflow + mz_extraction_window_unit string Th Th,ppm
OpenSwathWorkflow + out_qc output-file *.json
OpenSwathWorkflow + outer_loop_threads int -1
OpenSwathWorkflow + tr_irt input-file *.traML,*.tsv,*.pqp
OpenSwathWorkflow + tr_irt_nonlinear input-file *.traML,*.tsv,*.pqp
OpenSwathWorkflow + use_ms1_ion_mobility string true true,false
OpenSwathWorkflow - Debugging:irt_mzml string
OpenSwathWorkflow - Debugging:irt_trafo string
OpenSwathWorkflow - Scoring:TransitionGroupPicker:min_peak_width double 14
OpenSwathWorkflow - Scoring:stop_report_after_feature int -1
OpenSwathWorkflow - batchSize int 0 0:
OpenSwathWorkflow - irt_mz_extraction_window double 0.05
OpenSwathWorkflow - mz_correction_function string none none,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm
OpenSwathWorkflow - ppm string false true,false
OpenSwathWorkflow - ppm_irtwindow string false true,false
OpenSwathWorkflow - tr_irt input-file *.traML
PSMFeatureExtractor + out_type string mzid,idXML
PeptideIndexer + enzyme:name string Trypsin Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,iodosobenzoate,proline endopeptidase,2-iodobenzoate,Alpha-lytic protease,glutamyl endopeptidase
PeptideIndexer - enzyme:name string Trypsin Chymotrypsin/P,Arg-C/P,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,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
PercolatorAdapter + enzyme string trypsin no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp
PercolatorAdapter - enzyme string trypsin no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin
PrecursorIonSelector + dt_model input-file *.txt
PrecursorIonSelector + rt_model input-file *.txt
PrecursorIonSelector + sim_results output-file *.txt
PrecursorIonSelector - dt_model string
PrecursorIonSelector - rt_model string
PrecursorIonSelector - sim_results string
ProteinInference + Algorithm:min_peptides_per_protein int 1 0:
ProteinInference + Algorithm:score_aggregation_method string maximum maximum,product,sum
ProteinInference + Algorithm:skip_count_annotation string false
ProteinInference + Algorithm:treat_charge_variants_separately string true
ProteinInference + Algorithm:treat_modification_variants_separately string true
ProteinInference + Algorithm:use_shared_peptides string true
ProteinInference + Merging:annotate_origin string true true,false
ProteinInference + annotate_indist_groups string true true,false
ProteinInference + merge_runs string no no,all
ProteinInference - min_peptides_per_protein int 2 1:
ProteinInference - treat_charge_variants_separately string false true,false
ProteinInference - treat_modification_variants_separately string false true,false
ProteinQuantifier + best_charge_and_fraction string false true,false
ProteinQuantifier + design input-file *.tsv
ProteinQuantifier + greedy_group_resolution string false true,false
ProteinQuantifier + mztab output-file *.mzTab
ProteinQuantifier - filter_charge string false true,false
RNADigestor + cdna string false true,false
RNADigestor + enzyme string RNase_T1 RNase_U2,RNase_A,RNase_MC1,RNase_H,no cleavage,unspecific cleavage,RNase_T1,cusativin
RNADigestor - enzyme string RNase_T1 unspecific cleavage,no cleavage,RNase_T1
RNPxlSearch + RNPxl:nt_groups string
RNPxlSearch + RNPxl:only_xl string false true,false
RNPxlSearch + peptide:enzyme string Trypsin Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
RNPxlSearch - RNPxl:localization string false true,false
RNPxlSearch - peptide:enzyme string Trypsin Arg-C/P,Asp-N,Chymotrypsin/P,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Trypsin,Arg-C,Asp-N/B,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,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,Alpha-lytic protease
SimpleSearchEngine + Search:enzyme string Trypsin Asp-N/B,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SimpleSearchEngine + Search:fragment:mass_tolerance double 10.0
SimpleSearchEngine + Search:fragment:mass_tolerance_unit string ppm ppm,Da
SimpleSearchEngine + Search:modifications:fixed string ...
SimpleSearchEngine + Search:modifications:variable string ...
SimpleSearchEngine + Search:modifications:variable_max_per_peptide int 2
SimpleSearchEngine + Search:peptide:max_size int 40
SimpleSearchEngine + Search:peptide:min_size int 7
SimpleSearchEngine + Search:peptide:missed_cleavages int 1
SimpleSearchEngine + Search:peptide:motif string
SimpleSearchEngine + Search:precursor:isotopes int
SimpleSearchEngine + Search:precursor:mass_tolerance double 10.0
SimpleSearchEngine + Search:precursor:mass_tolerance_unit string ppm ppm,Da
SimpleSearchEngine + Search:precursor:max_charge int 5
SimpleSearchEngine + Search:precursor:min_charge int 2
SimpleSearchEngine + Search:report:top_hits int 1
SimpleSearchEngine - enzyme string Trypsin Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-N_ambic,Arg-C/P,unspecific cleavage,Arg-C,Asp-N/B,Asp-N,Trypsin
SimpleSearchEngine - fragment:mass_tolerance double 10
SimpleSearchEngine - fragment:mass_tolerance_unit string ppm ppm,Da
SimpleSearchEngine - modifications:fixed string ...
SimpleSearchEngine - modifications:variable string ...
SimpleSearchEngine - modifications:variable_max_per_peptide int 2
SimpleSearchEngine - peptide:max_size int 40
SimpleSearchEngine - peptide:min_size int 7
SimpleSearchEngine - peptide:missed_cleavages int 1
SimpleSearchEngine - peptide:motif string
SimpleSearchEngine - precursor:isotopes int
SimpleSearchEngine - precursor:mass_tolerance double 10
SimpleSearchEngine - precursor:mass_tolerance_unit string ppm ppm,Da
SimpleSearchEngine - precursor:max_charge int 5
SimpleSearchEngine - precursor:min_charge int 2
SimpleSearchEngine - report:top_hits int 1
SiriusAdapter + converter_mode string false true,false
SiriusAdapter + executable input-file sirius
SiriusAdapter + out_ms output-file *.ms
SiriusAdapter + out_workspace_directory string
SiriusAdapter + preprocessing:feature_only string false true,false
SiriusAdapter + preprocessing:filter_by_num_masstraces int 1 1:
SiriusAdapter + preprocessing:isotope_pattern_iterations int 3
SiriusAdapter + preprocessing:no_masstrace_info_isotope_pattern string false true,false
SiriusAdapter + preprocessing:precursor_mz_tolerance double 0.005
SiriusAdapter + preprocessing:precursor_mz_tolerance_unit string Da Da,ppm
SiriusAdapter + preprocessing:precursor_rt_tolerance int 5
SiriusAdapter + sirius:auto_charge string false true,false
SiriusAdapter + sirius:candidates int 5 1:
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 string false true,false
SiriusAdapter + sirius:isotope string both score,filter,both,omit
SiriusAdapter + sirius:most_intense_ms2 string false true,false
SiriusAdapter + sirius:no_recalibration string false true,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:
SiriusAdapter + sirius:tree_timeout int 0 0:
SiriusAdapter - auto_charge string false true,false
SiriusAdapter - candidates int 5
SiriusAdapter - compound_timeout int 10
SiriusAdapter - database string all all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda
SiriusAdapter - elements string CHNOP[5]S[8]Cl[1]
SiriusAdapter - executable input-file
SiriusAdapter - feature_only string false true,false
SiriusAdapter - filter_by_num_masstraces int 1 1:
SiriusAdapter - ion_tree string false true,false
SiriusAdapter - isotope string both score,filter,both,omit
SiriusAdapter - isotope_pattern_iterations int 3
SiriusAdapter - most_intense_ms2 string false true,false
SiriusAdapter - no_masstrace_info_isotope_pattern string false true,false
SiriusAdapter - no_recalibration string false true,false
SiriusAdapter - noise int 0
SiriusAdapter - ppm_max int 10
SiriusAdapter - precursor_mz_tolerance double 0.005
SiriusAdapter - precursor_mz_tolerance_unit string Da Da,ppm
SiriusAdapter - precursor_rt_tolerance double 5
SiriusAdapter - profile string qtof qtof,orbitrap,fticr
SiriusAdapter - top_n_hits int 10
SiriusAdapter - tree_timeout int 0
TextExporter + id:add_protein_hit_metavalues int -1 -1:100
TextExporter + id:protein_groups string false true,false
XFDR + maxborder double 50.0
XFDR + minborder double -50.0
XFDR + minscore double -10.0
XFDR - maxborder int -1
XFDR - minborder int -1
XFDR - minscore int 0
XTandemAdapter + enzyme string Trypsin 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,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,unspecific cleavage
XTandemAdapter - enzyme string Trypsin Arg-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,Asp-N,unspecific cleavage