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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 - 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 + deisotoping_annotate_charge bool false
AssayGeneratorMetabo - deisotoping:annotate_charge bool false
AssayGeneratorMetabo + deisotoping_fragment_tolerance double 1.0
AssayGeneratorMetabo - deisotoping:fragment_tolerance double 1.0
AssayGeneratorMetabo + deisotoping_fragment_unit string ppm ppm,Da
AssayGeneratorMetabo - deisotoping:fragment_unit string ppm ppm,Da
AssayGeneratorMetabo + deisotoping_keep_only_deisotoped bool false
AssayGeneratorMetabo - deisotoping:keep_only_deisotoped bool false
AssayGeneratorMetabo + deisotoping_max_charge int 1 1:
AssayGeneratorMetabo - deisotoping:max_charge int 1 1:
AssayGeneratorMetabo + deisotoping_max_isopeaks int 3 3:
AssayGeneratorMetabo - deisotoping:max_isopeaks int 3 3:
AssayGeneratorMetabo + deisotoping_min_charge int 1 1:
AssayGeneratorMetabo - deisotoping:min_charge int 1 1:
AssayGeneratorMetabo + deisotoping_min_isopeaks int 2 2:
AssayGeneratorMetabo - deisotoping:min_isopeaks int 2 2:
AssayGeneratorMetabo + deisotoping_use_deisotoper bool false
AssayGeneratorMetabo - deisotoping:use_deisotoper bool false
AssayGeneratorMetabo + feature_only string false false,true
AssayGeneratorMetabo + filter_by_num_masstraces int 1 1:
AssayGeneratorMetabo - fingerid:db string
AssayGeneratorMetabo - fragment_annotation_score_threshold double 0.8 0.0:1.0
AssayGeneratorMetabo - fragment_annotation string sirius none,sirius
AssayGeneratorMetabo + in_featureinfo input-file *.featureXML
AssayGeneratorMetabo - in_id input-file *.featureXML
AssayGeneratorMetabo - out_workspace_directory string
AssayGeneratorMetabo + precursor_consensus_spectrum_rt_tolerance double 5.0
AssayGeneratorMetabo + precursor_mz_tolerance double 10.0
AssayGeneratorMetabo + precursor_mz_tolerance_unit string ppm ppm,Da
AssayGeneratorMetabo + precursor_rt_tolerance double 5.0
AssayGeneratorMetabo - preprocessing:feature_only bool false
AssayGeneratorMetabo - preprocessing:filter_by_num_masstraces int 1 1:
AssayGeneratorMetabo - preprocessing:isotope_pattern_iterations int 3
AssayGeneratorMetabo - preprocessing:no_masstrace_info_isotope_pattern bool false
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:loglevel string
AssayGeneratorMetabo - project:maxmz int -1
AssayGeneratorMetabo - project:processors int 1
AssayGeneratorMetabo - project:q bool false
AssayGeneratorMetabo - read_sirius_stdout bool false
AssayGeneratorMetabo - sirius:candidates int 10 0:
AssayGeneratorMetabo - sirius:candidates_per_ion int 1
AssayGeneratorMetabo - sirius:compound_timeout int 100 0:
AssayGeneratorMetabo - sirius:db string none
AssayGeneratorMetabo - sirius:elements_considered string SBrClBSe
AssayGeneratorMetabo - sirius:elements_enforced string CHNOP
AssayGeneratorMetabo - sirius_executable input-file
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:ions_enforced string
AssayGeneratorMetabo - sirius:no_isotope_filter bool false
AssayGeneratorMetabo - sirius:no_isotope_score bool false
AssayGeneratorMetabo - sirius:no_recalibration bool false
AssayGeneratorMetabo - sirius:ppm_max double 10.0
AssayGeneratorMetabo - sirius:ppm_max_ms2 double 10.0
AssayGeneratorMetabo - sirius:profile string default default,qtof,orbitrap,fticr
AssayGeneratorMetabo - sirius:solver string CLP
AssayGeneratorMetabo - sirius:tree_timeout int 100 0:
AssayGeneratorMetabo - use_exact_mass bool false
CometAdapter - enzyme string Trypsin Asp-N,Trypsin,Arg-C,Chymotrypsin,CNBr,no cleavage,unspecific cleavage,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter + enzyme string Trypsin glutamyl endopeptidase,Arg-C/P,Asp-N,Trypsin,Arg-C,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
CometAdapter - PeptideIndexing:enzyme:name string auto auto,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
CometAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Trypsin,Arg-C,PepsinA,TrypChymo,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-N,Lys-C/P,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
CometAdapter - second_enzyme string Asp-N,Trypsin,Arg-C,Chymotrypsin,CNBr,no cleavage,unspecific cleavage,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter + second_enzyme string glutamyl endopeptidase,Arg-C/P,Asp-N,Trypsin,Arg-C,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
DecoyDatabase + enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,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,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DecoyDatabase - enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,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,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
Digestor + enzyme string Trypsin Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
Digestor - enzyme string Trypsin Trypsin,Arg-C,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,V8-E,leukocyte elastase,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,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DigestorMotif + enzyme string Trypsin Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
DigestorMotif - enzyme string Trypsin Trypsin,Arg-C,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,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,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D
FeatureFinderCentroided + algorithm:advanced:pseudo_rt_shift double 500.0 1.0:
FeatureFinderCentroided - algorithm:debug:pseudo_rt_shift double 500.0 1.0:
FeatureFinderCentroided - out_mzq output-file *.mzq
FileConverter - change_im_format string none none,concatenated,multiple_spectra,mixed
FileConverter - include_noise bool false
FileConverter - NET_executable input-file
FileConverter - no_peak_picking bool false
FileConverter - no_zlib_compression bool false
FileConverter + RawToMzML:include_noise bool false
FileConverter + RawToMzML:NET_executable input-file
FileConverter + RawToMzML:no_peak_picking bool false
FileConverter + RawToMzML:no_zlib_compression bool false
FileConverter + RawToMzML:ThermoRaw_executable input-file ThermoRawFileParser.exe *.exe
FileConverter - ThermoRaw_executable input-file ThermoRawFileParser.exe *.exe
FileFilter + spectra:remove_activation string 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,Electron transfer and collision-induced dissociation,Electron transfer and higher-energy collision dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,Bruker proprietary method
FileFilter - spectra:remove_activation string 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,Bruker proprietary method
FileFilter + spectra:select_activation string 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,Electron transfer and collision-induced dissociation,Electron transfer and higher-energy collision dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,Bruker proprietary method
FileFilter - spectra:select_activation string 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,Bruker proprietary method
FileInfo - out_tsv output-file *.csv
FileInfo + out_tsv output-file *.tsv
IDFileConverter + fasta_to_mzml:add_zp1_ions bool false
IDFileConverter + fasta_to_mzml:add_zp2_ions bool false
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Trypsin,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
IDFileConverter - fasta_to_mzml:enzyme string Trypsin staphylococcal protease/D,proline-endopeptidase/HKR,Trypsin,Arg-C,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,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter - in_silico_digestion:enzyme string Trypsin Trypsin,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Arg-C,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,Asp-N,Asp-N/B,Asp-N_ambic,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
IDFilter + in_silico_digestion:enzyme string Trypsin Trypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,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/P,PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
IDFilter - missed_cleavages:enzyme string Trypsin Trypsin,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Arg-C,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,Asp-N,Asp-N/B,Asp-N_ambic,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
IDFilter + missed_cleavages:enzyme string Trypsin Trypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,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/P,PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
IDMapper + in input-file *.featureXML,*.consensusXML
IDMapper - in input-file *.featureXML,*.consensusXML,*.mzq
IDMapper + out output-file *.featureXML,*.consensusXML
IDMapper - out output-file *.featureXML,*.consensusXML,*.mzq
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,Electron transfer and collision-induced dissociation,Electron transfer and higher-energy collision dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,any
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
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:gauss_width double 50.0
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:peak_width double -1.0
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:remove_overlapping_peaks string false false,true
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sgolay_frame_length int 15
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sgolay_polynomial_order int 3
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:signal_to_noise double 1.0 0.0:
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sn_bin_count int 30
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sn_win_len double 1000.0
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:use_gauss string true false,true
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:write_sn_log_messages bool false
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:gauss_width double 50.0
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:method string corrected legacy,corrected,crawdad
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:peak_width double -1.0
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:remove_overlapping_peaks string false false,true
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sgolay_frame_length int 15
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sgolay_polynomial_order int 3
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:signal_to_noise double 1.0 0.0:
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sn_bin_count int 30
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sn_win_len double 1000.0
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:use_gauss string true false,true
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:write_sn_log_messages bool false
MSFraggerAdapter + digest:search_enzyme_name string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,iodosobenzoate,Trypsin,Arg-C,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,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
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Arg-C,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,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 + PeptideIndexing:enzyme:name string auto auto,Lys-C,Lys-N,Trypsin,Arg-C,Lys-C/P,PepsinA,V8-E,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,TrypChymo,Trypsin/P,V8-DE,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
MSFraggerAdapter - PeptideIndexing:enzyme:name string auto auto,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,Arg-C,V8-DE,V8-E,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
MSGFPlusAdapter + min_peaks int 10 10:
MSGFPlusAdapter + PeptideIndexing:enzyme:name string auto auto,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,TrypChymo,Trypsin/P,V8-DE,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C,Arg-C/P,Lys-C/P,PepsinA,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
MSGFPlusAdapter - PeptideIndexing:enzyme:name string auto auto,no cleavage,unspecific cleavage,Trypsin,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Asp-N,Asp-N/B,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Formic_acid,Lys-C,Lys-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
NucleicAcidSearchEngine - oligo:enzyme string no cleavage mazF,colicin_E5,no cleavage,cusativin,RNase_A,RNase_MC1,RNase_H,unspecific cleavage,RNase_U2,RNase_T1
NucleicAcidSearchEngine + oligo:enzyme string no cleavage RNase_T1,RNase_T1_Phosphatase,cusativin,RNase_4,RNase_4p,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_U2,RNase_A,RNase_MC1,RNase_H
OpenPepXLLF + peptide:enzyme string Trypsin Arg-C,Arg-C/P,Asp-N,Trypsin,TrypChymo,Trypsin/P,V8-DE,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Lys-C/P,PepsinA,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,V8-E,leukocyte elastase,proline endopeptidase,Formic_acid,Lys-C,Lys-N
OpenPepXLLF - peptide:enzyme string Trypsin Trypsin,Arg-C,Arg-C/P,Asp-N,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Lys-C/P,PepsinA,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXL + peptide:enzyme string Trypsin 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,Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Arg-C,Arg-C/P,no cleavage,unspecific cleavage
OpenPepXL - peptide:enzyme string Trypsin Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Arg-C,Arg-C/P,Asp-N
OpenSwathAnalyzer + algorithm:Scores:use_peak_shape_metrics string false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:gauss_width double 50.0
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:peak_width double -1.0
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks string false false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length int 15
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order int 3
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise double 1.0 0.0:
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_bin_count int 30
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_win_len double 1000.0
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:use_gauss string true false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages bool false
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50.0
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1.0
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1.0 0.0:
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000.0
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true false,true
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages bool false
OpenSwathAnalyzer + algorithm:use_ms1_ion_mobility string true
OpenSwathRTNormalizer + algorithm:Scores:use_peak_shape_metrics string false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:gauss_width double 50.0
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:peak_width double -1.0
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks string false false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length int 15
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order int 3
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise double 1.0 0.0:
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_bin_count int 30
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_win_len double 1000.0
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:use_gauss string true false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages bool false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50.0
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1.0
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1.0 0.0:
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000.0
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true false,true
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages bool false
OpenSwathRTNormalizer + algorithm:use_ms1_ion_mobility string true
OpenSwathWorkflow + Scoring:Scores:use_peak_shape_metrics string false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:gauss_width double 30.0
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:peak_width double -1.0
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks string true false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length int 11
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order int 3
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise double 0.1 0.0:
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:use_gauss string false false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages bool false
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width double 30.0
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width double -1.0
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string true false,true
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 11
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 0.1 0.0:
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss string false false,true
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages bool false
OpenSwathWorkflow + Scoring:use_ms1_ion_mobility string true
PeptideIndexer - enzyme:name string auto auto,Arg-C/P,Asp-N,Asp-N/B,TrypChymo,Trypsin/P,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,V8-DE,V8-E,leukocyte elastase,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,Lys-C,Lys-N,Lys-C/P,PepsinA,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate
PeptideIndexer + enzyme:name string auto auto,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,TrypChymo,Trypsin/P,Trypsin,Arg-C,Lys-N,Lys-C/P,PepsinA,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,unspecific cleavage
RNADigestor - enzyme string RNase_T1 RNase_A,RNase_MC1,RNase_H,RNase_T1,RNase_U2,cusativin,mazF,colicin_E5,no cleavage,unspecific cleavage
RNADigestor + enzyme string RNase_T1 RNase_MC1,RNase_H,RNase_4,RNase_4p,cusativin,RNase_U2,RNase_A,RNase_T1,RNase_T1_Phosphatase,mazF,colicin_E5,no cleavage,unspecific cleavage
SageAdapter - enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C,Lys-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,proline-endopeptidase/HKR,Glu-C+P,Trypsin,Arg-C,unspecific cleavage,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,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage
SageAdapter + enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Asp-N,Asp-N/B,Trypsin,Arg-C,Glu-C+P,PepsinA + P,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,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
SageAdapter - PeptideIndexing:enzyme:name string auto auto,Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,TrypChymo,Trypsin/P,V8-DE,V8-E,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,Arg-C,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease
SageAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Arg-C/P,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,Asp-N,Asp-N/B,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,Lys-C/P,PepsinA
SimpleSearchEngine + Search:enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Trypsin,Asp-N,Asp-N/B,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Chymotrypsin/P,CNBr,Formic_acid,Asp-N_ambic,Chymotrypsin,TrypChymo,Trypsin/P,Lys-C/P,PepsinA,Lys-C,Lys-N
SimpleSearchEngine - Search:enzyme string Trypsin Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Arg-C,Arg-C/P,Trypsin,CNBr,Formic_acid,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,Lys-C/P,PepsinA,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P
SpecLibSearcher - compare_function string ZhangSimilarityScore PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore
SpecLibSearcher + compare_function string ZhangSimilarityScore ZhangSimilarityScore,SpectraSTSimilarityScore
XTandemAdapter - enzyme string Trypsin Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C,Arg-C/P,Asp-N,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,no cleavage,unspecific cleavage,Trypsin,V8-DE,V8-E,leukocyte elastase,Formic_acid,Lys-C,Lys-N
XTandemAdapter + enzyme string Trypsin Lys-N,Lys-C/P,PepsinA,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Trypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,Arg-C,Arg-C/P,Asp-N,no cleavage,unspecific cleavage
XTandemAdapter - PeptideIndexing:enzyme:name string auto auto,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C,Arg-C/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Formic_acid,Lys-C,Lys-N
XTandemAdapter + PeptideIndexing:enzyme:name string auto auto,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C,Arg-C/P,Lys-C/P,PepsinA,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Lys-C,Lys-N,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin,unspecific cleavage,Asp-N,Asp-N/B,Asp-N_ambic