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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
AssayGeneratorMetabo + fingerid:db string
AssayGeneratorMetabo + project:loglevel string
AssayGeneratorMetabo + project:maxmz int -1
AssayGeneratorMetabo + read_sirius_stdout bool false
AssayGeneratorMetabo + sirius:candidates int 10 0:
AssayGeneratorMetabo + sirius:candidates_per_ion int 1
AssayGeneratorMetabo + sirius:db string none
AssayGeneratorMetabo + sirius:elements_considered string SBrClBSe
AssayGeneratorMetabo + sirius:elements_enforced string CHNOP
AssayGeneratorMetabo + sirius:formulas string
AssayGeneratorMetabo + sirius:ions_considered string [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-
AssayGeneratorMetabo + sirius:profile string default default,qtof,orbitrap,fticr
AssayGeneratorMetabo + sirius:solver string CLP
AssayGeneratorMetabo + sirius:tree_timeout int 100 0:
AssayGeneratorMetabo - fingerid:candidates int 10 1:
AssayGeneratorMetabo - fingerid:db string BIO
AssayGeneratorMetabo - sirius:candidates int 5 1:
AssayGeneratorMetabo - sirius:candidates_per_ion int -1
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:profile string qtof default,qtof,orbitrap,fticr
AssayGeneratorMetabo - sirius:tree_timeout int 0 0:
CometAdapter + PeptideIndexing:allow_nterm_protein_cleavage string true true,false
CometAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
CometAdapter + enzyme string Trypsin Trypsin,Arg-C,Chymotrypsin,CNBr,Asp-N,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage
CometAdapter + second_enzyme string Trypsin,Arg-C,Chymotrypsin,CNBr,Asp-N,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage
CometAdapter - PeptideIndexing:enzyme:name string auto auto,Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
CometAdapter - enzyme string Trypsin Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage
CometAdapter - second_enzyme string Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage
CompNovo + algorithm:tryptic_only string true true,false
CompNovo - algorithm:tryptic_only string true
CompNovoCID + algorithm:tryptic_only string true true,false
CompNovoCID - algorithm:tryptic_only string true
DecoyDatabase + enzyme string Trypsin Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
DecoyDatabase - enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
Digestor + enzyme string Trypsin Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
Digestor - enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
DigestorMotif + enzyme string Trypsin Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,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,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
FalseDiscoveryRate + peptide bool false
FeatureFinderIdentification + min_psm_cutoff string none
FeatureFinderIdentification + svm:log2_p double
FeatureFinderMetaboIdent + candidates_out output-file
FeatureFinderMetaboIdent - candidates_out output-file *.featureXML
FidoAdapter + accuracy string best best,relaxed,sloppy
FidoAdapter - accuracy string ,best,relaxed,sloppy
FileConverter + include_noise bool false
FileConverter + no_zlib_compression bool false
FileFilter + f_and_c:remove_hull bool false
GNPSExport + out_meta_values output-file *.tsv
GNPSExport + out_pairs output-file *.csv
GNPSExport + out_quantification output-file *.txt
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Chymotrypsin,Trypsin,Arg-C,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFileConverter - fasta_to_mzml:enzyme string Trypsin Asp-N,Asp-N/B,Asp-N_ambic,Trypsin,Arg-C,Arg-C/P,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,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
IDFilter + in_silico_digestion:enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter + missed_cleavages:enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter - in_silico_digestion:enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter - missed_cleavages:enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDRipper + out output-prefix
IDRipper - out output-file
IsobaricAnalyzer + extraction:select_activation string auto auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,any
IsobaricAnalyzer + tmt18plex:channel_126_description string
IsobaricAnalyzer + tmt18plex:channel_127C_description string
IsobaricAnalyzer + tmt18plex:channel_127N_description string
IsobaricAnalyzer + tmt18plex:channel_128C_description string
IsobaricAnalyzer + tmt18plex:channel_128N_description string
IsobaricAnalyzer + tmt18plex:channel_129C_description string
IsobaricAnalyzer + tmt18plex:channel_129N_description string
IsobaricAnalyzer + tmt18plex:channel_130C_description string
IsobaricAnalyzer + tmt18plex:channel_130N_description string
IsobaricAnalyzer + tmt18plex:channel_131C_description string
IsobaricAnalyzer + tmt18plex:channel_131N_description string
IsobaricAnalyzer + tmt18plex:channel_132C_description string
IsobaricAnalyzer + tmt18plex:channel_132N_description string
IsobaricAnalyzer + tmt18plex:channel_133C_description string
IsobaricAnalyzer + tmt18plex:channel_133N_description string
IsobaricAnalyzer + tmt18plex:channel_134C_description string
IsobaricAnalyzer + tmt18plex:channel_134N_description string
IsobaricAnalyzer + tmt18plex:channel_135N_description string
IsobaricAnalyzer + tmt18plex:correction_matrix string
IsobaricAnalyzer + tmt18plex:reference_channel string 126 126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C,132N,132C,133N,133C,134N,134C,135N
IsobaricAnalyzer + type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt18plex,tmt6plex
IsobaricAnalyzer - extraction:select_activation string auto auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,
IsobaricAnalyzer - type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt6plex
MSFraggerAdapter + PeptideIndexing:allow_nterm_protein_cleavage string true true,false
MSFraggerAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,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 unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage
MSFraggerAdapter - PeptideIndexing:enzyme:name string auto auto,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin,Arg-C,Arg-C/P,unspecific cleavage
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
MSGFPlusAdapter + PeptideIndexing:allow_nterm_protein_cleavage string true true,false
MSGFPlusAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
MSGFPlusAdapter - PeptideIndexing:enzyme:name string auto auto,Trypsin,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,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
MSGFPlusAdapter - add_decoys bool false
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
MapAlignerIdentification + model:linear:x_weight string x 1/x,1/x2,ln(x),x
MapAlignerIdentification + model:linear:y_weight string y 1/y,1/y2,ln(y),y
MapAlignerIdentification - model:linear:x_weight string 1/x,1/x2,ln(x),
MapAlignerIdentification - model:linear:y_weight string 1/y,1/y2,ln(y),
MapAlignerSpectrum + model:linear:x_weight string x 1/x,1/x2,ln(x),x
MapAlignerSpectrum + model:linear:y_weight string y 1/y,1/y2,ln(y),y
MapAlignerSpectrum - model:linear:x_weight string 1/x,1/x2,ln(x),
MapAlignerSpectrum - model:linear:y_weight string 1/y,1/y2,ln(y),
MapAlignerTreeGuided + algorithm:model:linear:x_weight string x 1/x,1/x2,ln(x),x
MapAlignerTreeGuided + algorithm:model:linear:y_weight string y 1/y,1/y2,ln(y),y
MapAlignerTreeGuided - algorithm:model:linear:x_weight string 1/x,1/x2,ln(x),
MapAlignerTreeGuided - algorithm:model:linear:y_weight string 1/y,1/y2,ln(y),
MapRTTransformer + model:linear:x_weight string x 1/x,1/x2,ln(x),x
MapRTTransformer + model:linear:y_weight string y 1/y,1/y2,ln(y),y
MapRTTransformer - model:linear:x_weight string 1/x,1/x2,ln(x),
MapRTTransformer - model:linear:y_weight string 1/y,1/y2,ln(y),
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:negative_mode bool false
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:use_minority_bound string true true,false
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:negative_mode string false
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:use_minority_bound string true
MetaboliteSpectralMatcher + algorithm:merge_spectra string true true,false
MetaboliteSpectralMatcher + database input-file *.mzML,*.msp,*.mgf
MetaboliteSpectralMatcher + out_spectra output-file *.mzML
MetaboliteSpectralMatcher - database input-file *.mzML
MzMLSplitter + out output-prefix
MzMLSplitter - out string
NoiseFilterGaussian + algorithm:write_log_messages bool false
NoiseFilterGaussian - algorithm:write_log_messages string false
NucleicAcidSearchEngine + modifications:variable string io6A,s2U,k2C,m2Gm,Ym,f5Cm,Qbase,ac4Cm,imG-14,cm5s2U,mnm5s2U,m227G,yW-58,I,g6A,nm5U,m7G,s2Um,Y,hm5C,m5U,preQ0,o2yW,m5Um,preQ1,m66Am,ac6A,ms2io6A,Am,Im,mnm5U,m22G,t6A,m8A,m7GpppN,m27GpppN,m227GpppN,mpppN,m28A,acp3D,acp3Y,imG,D,N,C+,m27Gm,ho5C,inm5U,inm5Um,inm5s2U,pppN,GpppN,CoApN,m44C,acCoApN,malonyl-CoApN,succinyl-CoApN,ppN,NADpN,m6t6A,OHyWy,pG(pN),ncm5s2U,nchm5U,mchm5Um,pN,ges2U,cmnm5ges2U,mnm5ges2U,nm5ges2U,m5D,mmpN,mpN,5'-OH-N,N2'3'cp,ct6A,hm6A,f6A,cnm5U,mcmo5Um,m5C,ms2ct6A,ht6A,msms2i6A,hm5Cm,pY,pm5C,ps2U,hn6A,pD,pm2G,pm66A,pGm,pm5U,pm22G,pm3U,m5Cm,Ar(p),pac4C,pCm,pppG,pm7G,pm1A,pUm,pAm,pm4Cm,pC2'3'cp,tm5U,pm6A,pyW,pm1G,pA2'3'cp,ps4U,pI,ppG,pm2A,m1G,pmcm5s2U,cmnm5Um,pse2U,pt6A,pf5C,pppA,pG,pG2'3'cp,pms2i6A,pcmo5U,pyW,Xm,pm44C,pi6A,phm5C,pU,pAr(p),pac4Cm,pGp,m1I,pU2'3'cp,mcm5U,Gm,pm4C,ncm5Um,pm5Um,pmnm5U,pm3C,m5s2U,yW,pC,pm6t6A,f5C,pAp,m1Am,m1Im,ApppN,AppppN,ApppppN,m6ApppN,m6AppppN,m6ApppppN,m7GppppN,Gr(p),pm1Am,pm1Gm,pm1Im,pm1acp3Y,pm1I,pm1Y,pk2C,ps2C,pm1acp3Y,pm3Y,nm5s2U,pm5Cm,pmchm5U,pinm5Um,pinm5s2U,pinm5U,pnm5U,pncm5U,pchm5U,pcmnm5U,pcm5U,m2G,pho5U,pmcm5Um,pmcm5U,pmo5U,pm5D,pmimG,phm5Cm,pIm,pYm,pmcmo5Um,m2A,pGr(p),pm28A,pmsms2i6A,pges2U,pms2ct6A,pms2io6A,pms2hn6A,pms2m6A,pms2t6A,ps2Um,pm3Um,pacp3D,pacp3U,pimG-14,pmchm5Um,pnm5ges2U,pnm5se2U,pnm5s2U,pnchm5U,pncm5Um,m4Cm,pncm5s2U,pcm5s2U,pcmnm5Um,pcmnm5ges2U,pcmnm5se2U,pcmnm5s2U,pcnm5U,pf5Cm,pho5C,pm5s2U,m27G,m22Gm,pmnm5ges2U,pmnm5se2U,pmnm5s2U,ptm5s2U,ptm5U,pyW-86,pyW-72,pyW-58,ppreQ1,ppreQ0,m66A,pm8A,pC+,pG+,pct6A,poQ,pgalQ,pgluQ,pht6A,pOHyW,pimG2,gluQ,pmanQ,pOHyWy,pm27Gm,pQ,pOHyWx,pmcmo5U,pimG,pm44Cm,pm2Gm,pm22Gm,ncm5U,pm6Am,pm66Am,pio6A,pac6A,pf6A,pg6A,phm6A,phn6A,cm5U,pm27G,pm227G,pm27Gm,pA,cmnm5s2U,cmo5U,m3Y,m3U,ms2m6A,Um,ms2i6A,m3C,cmnm5se2U,ms2t6A,i6A,m3Um,mcmo5U,mimG,oQ,preQ1base,nm5se2U,m1Gm,ho5U,Q,xG,mcm5s2U,m44Cm,s4U,xC,yW-86,xA,chm5U,mo5U,acp3U,xU,yW-72,mnm5se2U,ms2hn6A,m1acp3Y,mcm5Um,ac4C,m6Am,m1A,Cm,mchm5U,galQ,cmnm5U,m1Y,imG2,m4C,manQ,tm5s2U,s2C,OHyWx,se2U,preQ0base,m6A,OHyW,xX,G+,3'-p,5'-p,5'-p*,3'-c,mA,mC,mG,mU,sU,mmA,mAm,mCm,mGm,mUm,cmo5U/chm5U,mchm5U/mcmo5U,mchm5Um/mcmo5Um,m6t6A/hn6A,galQ/manQ,mA?,mC?,mG?,mU?,mI?,msU?,mmA?,mmC?,mmG?,mmmG?,ac4C/f5Cm?,acp3U/cmnm5Um?,dA,dC,dG,dU,dT,A*,C*,G*,U*,dA*,dC*,dG*,dU*,dT*
NucleicAcidSearchEngine - modifications:variable string m1Am,m1Gm,m1Im,m1acp3Y,m1A,m1G,m1I,m1Y,m28A,msms2i6A,ges2U,k2C,m2A,ms2ct6A,ms2io6A,ms2hn6A,ms2i6A,ms2m6A,ms2t6A,se2U,s2Um,s2C,s2U,Am,Cm,Gm,Im,Ym,Um,mcmo5Um,Ar(p),Gr(p),(pN)2'3'>p,hm5Cm,m3Um,acp3D,acp3Y,acp3U,m3C,m3Y,m3U,imG-14,s4U,m5Cm,m5Um,mchm5Um,mchm5U,inm5s2U,inm5Um,inm5U,nm5ges2U,nm5se2U,nm5s2U,nm5U,nchm5U,ncm5s2U,ncm5Um,ncm5U,chm5U,cm5s2U,cmnm5ges2U,cmnm5se2U,cmnm5s2U,cmnm5Um,cmnm5U,cm5U,cnm5U,f5Cm,f5C,ho5C,hm5C,ho5U,mcm5s2U,mcm5Um,mcm5U,mo5U,m5s2U,mnm5ges2U,mnm5se2U,mnm5s2U,mnm5U,m5C,m5D,m5U,tm5s2U,tm5U,CoA(pN),acCoA(pN),malonyl-CoA(pN),succinyl-CoA(pN),p(pN),5'-OH-N,(pN),NAD(pN),pp(pN),yW-86,yW-72,yW-58,preQ1tRNA,preQ0tRNA,m7G,m7Gpp(pN),m8A,m2Gm,m27Gm,m27G,m27Gpp(pN),m22Gm,m227G,m227Gpp(pN),m22G,m2G,m4Cm,m44Cm,m44C,ac4Cm,ac4C,m4C,m6Am,m66Am,m66A,io6A,ac6A,f6A,g6A,hm6A,hn6A,i6A,m6t6A,m6A,t6A,Qbase,C+,mm(pN),m(pN),G+,ct6A,D,oQ,galQ,mpp(pN),gluQ,pG(pN),Gpp(pN),ht6A,OHyW,I,imG2,manQ,OHyWy,mimG,o2yW,preQ0base,preQ1base,Y,Q,OHyWx,Xm,xX,xA,xC,xG,xU,N,cmo5U,mcmo5U,yW,imG,dA,dC,dG,dU,dT,3'-p,5'-p,mA,mC,mG,mU,sU,mmA,mAm,mCm,mGm,mUm,cmo5U/chm5U,mchm5U/mcmo5U,mchm5Um/mcmo5Um,m6t6A/hn6A,galQ/manQ,mA?,mC?,mG?,mU?,mI?,msU?,mmA?,mmC?,mmG?,mmmG?,ac4C/f5Cm?,acp3U/cmnm5Um?
OpenPepXL + peptide:enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXL - peptide:enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXLLF + peptide:enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXLLF - peptide:enzyme string Trypsin 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,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenSwathAnalyzer + algorithm:strict string true true,false
OpenSwathAnalyzer - algorithm:strict string true
OpenSwathFileSplitter + outputDirectory output-prefix ./
OpenSwathFileSplitter - outputDirectory string ./
OpenSwathRTNormalizer + algorithm:strict string true true,false
OpenSwathRTNormalizer - algorithm:strict string true
OpenSwathWorkflow + Scoring:strict string true true,false
OpenSwathWorkflow + pasef bool false
OpenSwathWorkflow - Scoring:strict string true
PeptideIndexer + allow_nterm_protein_cleavage string true true,false
PeptideIndexer + enzyme:name string auto auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
PeptideIndexer - enzyme:name string auto auto,Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
PrecursorIonSelector + algorithm:Preprocessing:store_peptide_sequences bool false
PrecursorIonSelector - algorithm:Preprocessing:store_peptide_sequences string false
ProteinQuantifier + method string top top,iBAQ
ProteinQuantifier + top:N int 3 0:
ProteinQuantifier + top:aggregate string median median,mean,weighted_mean,sum
ProteinQuantifier + top:include_all bool false
ProteinQuantifier - average string median median,mean,weighted_mean,sum
ProteinQuantifier - include_all bool false
ProteinQuantifier - top int 3 0:
ProteomicsLFQ + Alignment:model:linear:x_weight string x 1/x,1/x2,ln(x),x
ProteomicsLFQ + Alignment:model:linear:y_weight string y 1/y,1/y2,ln(y),y
ProteomicsLFQ + FDR_type string PSM PSM,PSM+peptide
ProteomicsLFQ + PeptideQuantification:min_psm_cutoff string none
ProteomicsLFQ + PeptideQuantification:svm:log2_p double
ProteomicsLFQ + ProteinQuantification:method string top top,iBAQ
ProteomicsLFQ + ProteinQuantification:top:N int 3 0:
ProteomicsLFQ + ProteinQuantification:top:aggregate string median median,mean,weighted_mean,sum
ProteomicsLFQ + ProteinQuantification:top:include_all string true true,false
ProteomicsLFQ + picked_proteinFDR bool false
ProteomicsLFQ - Alignment:model:linear:x_weight string 1/x,1/x2,ln(x),
ProteomicsLFQ - Alignment:model:linear:y_weight string 1/y,1/y2,ln(y),
ProteomicsLFQ - ProteinQuantification:average string median median,mean,weighted_mean,sum
ProteomicsLFQ - ProteinQuantification:include_all string true true,false
ProteomicsLFQ - ProteinQuantification:top int 3 0:
ProteomicsLFQ - picked_proteinFDR string false
QualityControl + in_fasta input-file *.fasta
QualityControl + out_msms string
RNPxlSearch + peptide:enzyme string Trypsin Arg-C,Trypsin,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
RNPxlSearch - peptide:enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SimpleSearchEngine + Search:enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SimpleSearchEngine - Search:enzyme string Trypsin Trypsin,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,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SiriusAdapter + fingerid:db string
SiriusAdapter + out_annotated_spectra output-file *.mzML
SiriusAdapter + project:loglevel string
SiriusAdapter + project:maxmz int -1
SiriusAdapter + read_sirius_stdout bool false
SiriusAdapter + sirius:candidates int 10 0:
SiriusAdapter + sirius:candidates_per_ion int 1
SiriusAdapter + sirius:db string none
SiriusAdapter + sirius:elements_considered string SBrClBSe
SiriusAdapter + sirius:elements_enforced string CHNOP
SiriusAdapter + sirius:formulas string
SiriusAdapter + sirius:ions_considered string [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-
SiriusAdapter + sirius:profile string default default,qtof,orbitrap,fticr
SiriusAdapter + sirius:solver string CLP
SiriusAdapter + sirius:tree_timeout int 100 0:
SiriusAdapter + sirius_user_email string
SiriusAdapter + sirius_user_password string
SiriusAdapter - fingerid:candidates int 10 1:
SiriusAdapter - fingerid:db string BIO
SiriusAdapter - project:processors int 1
SiriusAdapter - sirius:candidates int 5 1:
SiriusAdapter - sirius:candidates_per_ion int -1
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:profile string qtof default,qtof,orbitrap,fticr
SiriusAdapter - sirius:tree_timeout int 0 0:
SpectraMerger + algorithm:average_gaussian:ms_level int 1 0:
SpectraMerger + algorithm:average_gaussian:precursor_mass_tol double 0.0 0.0:
SpectraMerger + algorithm:average_gaussian:precursor_max_charge int 1 1:
SpectraMerger + algorithm:average_tophat:ms_level int 1 0:
SpectraMerger + algorithm:precursor_method:mass_tolerance double 0.0 0.0:
SpectraMerger - algorithm:average_gaussian:ms_level int 1 1:
SpectraMerger - algorithm:average_tophat:ms_level int 1 1:
TextExporter + consensus:add_metavalues bool false
XTandemAdapter + PeptideIndexing:allow_nterm_protein_cleavage string true true,false
XTandemAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
XTandemAdapter + enzyme string Trypsin Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,no cleavage,unspecific cleavage
XTandemAdapter - PeptideIndexing:enzyme:name string auto auto,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,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,V8-DE,V8-E,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Trypsin
XTandemAdapter - enzyme string Trypsin Asp-N,Asp-N/B,Asp-N_ambic,unspecific cleavage,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,Arg-C