
- 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	
