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CHANGELOG_PARAMS
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- ADDED:
- REMOVED:
- CHANGED PARAMETERS:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
CometAdapter + enzyme string Trypsin Arg-C/P,Asp-N,no cleavage,unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter - enzyme string Trypsin Arg-C/P,Asp-N,no cleavage,unspecific cleavage,Trypsin,Arg-C,leukocyte elastase,Chymotrypsin,CNBr,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter - PeptideIndexing:enzyme:name string auto auto,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C,Lys-N,Lys-C/P,PepsinA,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,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Arg-C,Arg-C/P
CometAdapter + PeptideIndexing:enzyme:name string auto auto,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Lys-C/P,PepsinA,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P
CometAdapter + second_enzyme string Arg-C/P,Asp-N,no cleavage,unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter - second_enzyme string Arg-C/P,Asp-N,no cleavage,unspecific cleavage,Trypsin,Arg-C,leukocyte elastase,Chymotrypsin,CNBr,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin/P,glutamyl endopeptidase
DigestorMotif + enzyme string Trypsin no cleavage,unspecific cleavage,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,V8-DE,V8-E,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
DigestorMotif - enzyme string Trypsin unspecific cleavage,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin,Arg-C,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,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,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease
FalseDiscoveryRate - protein_base_score_orientation string higher_better,lower_better
FalseDiscoveryRate - protein_base_score string
FalseDiscoveryRate - proteingroup bool false
FalseDiscoveryRate - protein_score string MS:1001492,Mascot,OMSSA,SEQUEST:xcorr,XTandem,hyperscore,ln(hyperscore),mvh,svm,E-Value,MS:1002053,MS:1002257,SpecEValue,evalue,expect,Posterior Probability,MS:1001493,Posterior Error Probability,pep,FDR,false discovery rate,fdr,MS:1001491,q-Value,q-value,qval,qvalue
FalseDiscoveryRate - PSM_peptide_base_score_orientation string higher_better,lower_better
FalseDiscoveryRate - PSM_peptide_base_score string
FeatureFinderIdentification - debug int 0
FeatureFinderIdentification + debug int 0 0:
FeatureFinderMetabo - algorithm:ffm:report_smoothed_intensities string true false,true
FeatureFinderMetaboIdent - debug int 0
FeatureFinderMetaboIdent + debug int 0 0:
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.sqMass,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.sqMass,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.mzTab,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo + in_type string mzData,mzXML,mzML,sqMass,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp
FileInfo - in_type string mzData,mzXML,mzML,sqMass,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,mzTab,fid,mzid,trafoXML,fasta,pqp
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Trypsin,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,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 leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,V8-DE,V8-E,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,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D
IDFilter - in_silico_digestion:enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Arg-C,Arg-C/P,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic
IDFilter + in_silico_digestion:enzyme string Trypsin Trypsin,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Formic_acid,Lys-C,Lys-N,Lys-C/P,Arg-C,Arg-C/P,Asp-N,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,PepsinA,TrypChymo,Trypsin/P,V8-DE,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr
IDFilter - missed_cleavages:enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Arg-C,Arg-C/P,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic
IDFilter + missed_cleavages:enzyme string Trypsin Trypsin,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Formic_acid,Lys-C,Lys-N,Lys-C/P,Arg-C,Arg-C/P,Asp-N,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,PepsinA,TrypChymo,Trypsin/P,V8-DE,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr
IDFilter - score:peptide double NaN
IDFilter + score:protein double nan
IDFilter - score:protein double NaN
IDFilter + score:proteingroup double nan
IDFilter - score:proteingroup double NaN
IDFilter + score:psm double nan
IDFilter - score:psm double NaN
IDFilter - score:type_peptide string MS:1001492,Mascot,OMSSA,SEQUEST:xcorr,XTandem,hyperscore,ln(hyperscore),mvh,svm,E-Value,MS:1002053,MS:1002257,SpecEValue,evalue,expect,Posterior Probability,MS:1001493,Posterior Error Probability,pep,FDR,false discovery rate,fdr,MS:1001491,q-Value,q-value,qval,qvalue
IDFilter - score:type_protein string MS:1001492,Mascot,OMSSA,SEQUEST:xcorr,XTandem,hyperscore,ln(hyperscore),mvh,svm,E-Value,MS:1002053,MS:1002257,SpecEValue,evalue,expect,Posterior Probability,MS:1001493,Posterior Error Probability,pep,FDR,false discovery rate,fdr,MS:1001491,q-Value,q-value,qval,qvalue
IsobaricAnalyzer - extraction:reporter_mass_shift double 2.0000000000000000e-03 1.0e-04:0.5
IsobaricAnalyzer + extraction:reporter_mass_shift double 2.0e-03 1.0e-04:0.5
MapAlignerPoseClustering - algorithm:superimposer:scaling_bucket_size double 5.0000000000000000e-03 0.0:
MapAlignerPoseClustering + algorithm:superimposer:scaling_bucket_size double 5.0e-03 0.0:
MSFraggerAdapter - PeptideIndexing:enzyme:name string auto auto,Lys-C,Lys-N,Trypsin,Arg-C,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Chymotrypsin/P,CNBr,Formic_acid,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
MSFraggerAdapter + PeptideIndexing:enzyme:name string auto auto,Lys-C,Lys-N,Trypsin,Arg-C,TrypChymo,Trypsin/P,V8-DE,V8-E,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Lys-C/P,PepsinA,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
MSGFPlusAdapter - PeptideIndexing:enzyme:name string auto auto,Asp-N,Asp-N/B,Asp-N_ambic,Trypsin,Arg-C,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,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,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid
MSGFPlusAdapter + PeptideIndexing:enzyme:name string auto auto,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Arg-C,Arg-C/P,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Lys-N,Lys-C/P,PepsinA,TrypChymo
NucleicAcidSearchEngine - oligo:enzyme string no cleavage cusativin,RNase_H,RNase_4,RNase_4p,mazF,colicin_E5,no cleavage,RNase_T1_Phosphatase,RNase_T1,unspecific cleavage,RNase_U2,RNase_A,RNase_MC1
NucleicAcidSearchEngine + oligo:enzyme string no cleavage RNase_4p,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_T1_Phosphatase,RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,RNase_4
OpenPepXLLF + peptide:enzyme string Trypsin Asp-N,Asp-N/B,Asp-N_ambic,Trypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Arg-C/P,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXLLF - peptide:enzyme string Trypsin Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr
OpenPepXL + peptide:enzyme string Trypsin Asp-N,Asp-N/B,Asp-N_ambic,Trypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Arg-C/P,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXL - peptide:enzyme string Trypsin Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr
OpenSwathAnalyzer - algorithm:spacing_for_spectra_resampling double 5.0000000000000000e-03 0.0:
OpenSwathAnalyzer + algorithm:spacing_for_spectra_resampling double 5.0e-03 0.0:
OpenSwathRTNormalizer - algorithm:spacing_for_spectra_resampling double 5.0000000000000000e-03 0.0:
OpenSwathRTNormalizer + algorithm:spacing_for_spectra_resampling double 5.0e-03 0.0:
OpenSwathWorkflow - Scoring:spacing_for_spectra_resampling double 5.0000000000000000e-03 0.0:
OpenSwathWorkflow + Scoring:spacing_for_spectra_resampling double 5.0e-03 0.0:
PeptideIndexer - enzyme:name string auto auto,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,leukocyte elastase,proline endopeptidase,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,V8-DE,V8-E,Arg-C/P,Asp-N,Asp-N/B,TrypChymo,Trypsin/P,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
PeptideIndexer + enzyme:name string auto auto,V8-DE,V8-E,unspecific cleavage,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Asp-N/B,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
QualityControl + out_evd string
QualityControl + out_msms string
QualityControl - out_txt:directory string
QualityControl - out_txt:omit_mq_evidence bool false
QualityControl - out_txt:omit_mq_msms bool false
RNADigestor - enzyme string RNase_T1 RNase_T1,RNase_A,RNase_MC1,RNase_H,RNase_U2,cusativin,RNase_T1_Phosphatase,RNase_4,RNase_4p,mazF,colicin_E5,no cleavage,unspecific cleavage
RNADigestor + enzyme string RNase_T1 RNase_U2,RNase_A,RNase_MC1,RNase_T1,cusativin,RNase_T1_Phosphatase,RNase_H,RNase_4,RNase_4p,mazF,colicin_E5,no cleavage,unspecific cleavage
SageAdapter - annotate_matches string true
SageAdapter - chimera string false
SageAdapter - deisotope string false
SageAdapter + enzyme string Trypsin proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,Arg-C,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SageAdapter - enzyme string Trypsin proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,Arg-C,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,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SageAdapter - PeptideIndexing:enzyme:name string auto auto,Arg-C,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Trypsin,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,no cleavage,unspecific cleavage,Lys-C/P,PepsinA
SageAdapter + PeptideIndexing:enzyme:name string auto auto,Arg-C/P,Asp-N,Asp-N/B,Formic_acid,Lys-C,Lys-N,Lys-C/P,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Trypsin,Arg-C,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D
SageAdapter - predict_rt string false
SageAdapter - q_value_threshold double 1.0
SageAdapter - smoothing string true
SageAdapter - wide_window string false
SimpleSearchEngine - Search:enzyme string Trypsin Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Arg-C,Arg-C/P
SimpleSearchEngine + Search:enzyme string Trypsin PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Lys-N,Lys-C/P,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Trypsin,Arg-C,CNBr,Formic_acid,Lys-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,proline endopeptidase,glutamyl endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P
XTandemAdapter - enzyme string Trypsin Arg-C,Arg-C/P,Asp-N,no cleavage,unspecific cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Trypsin,Lys-N,Lys-C/P,PepsinA,TrypChymo,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Asp-N/B,Asp-N_ambic,Chymotrypsin
XTandemAdapter + enzyme string Trypsin 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,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,no cleavage,unspecific cleavage
XTandemAdapter + PeptideIndexing:enzyme:name string auto auto,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,V8-E,leukocyte elastase,proline endopeptidase,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C,Lys-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,TrypChymo,Trypsin/P,V8-DE
XTandemAdapter - PeptideIndexing:enzyme:name string auto auto,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B,Arg-C,Arg-C/P,Trypsin,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,PepsinA,TrypChymo,Lys-N,Lys-C/P,leukocyte elastase,proline endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P