Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AccurateMassSearch	+	algorithm:mzTab:exportIsotopeIntensities	string	false	false,true	
AccurateMassSearch	+	algorithm:use_feature_adducts	string	false	false,true	
AccurateMassSearch	-	algorithm:mzTab:exportIsotopeIntensities	int	0	0:	
AssayGeneratorMetabo	+	deisotoping:annotate_charge	string	false	true,false	
AssayGeneratorMetabo	+	deisotoping:fragment_tolerance	double	1.0		
AssayGeneratorMetabo	+	deisotoping:fragment_unit	string	ppm	ppm,Da	
AssayGeneratorMetabo	+	deisotoping:keep_only_deisotoped	string	false	true,false	
AssayGeneratorMetabo	+	deisotoping:max_charge	int	1	1:	
AssayGeneratorMetabo	+	deisotoping:max_isopeaks	int	3	3:	
AssayGeneratorMetabo	+	deisotoping:min_charge	int	1	1:	
AssayGeneratorMetabo	+	deisotoping:min_isopeaks	int	2	2:	
AssayGeneratorMetabo	+	deisotoping:use_deisotoper	string	false	true,false	
AssayGeneratorMetabo	+	exclude_ms2_precursor	string	false	true,false	
AssayGeneratorMetabo	+	executable	input-file			
AssayGeneratorMetabo	+	fragment_annotation	string	none	none,sirius
AssayGeneratorMetabo	+	max_transitions	int	6		
AssayGeneratorMetabo	+	min_transitions	int	3		
AssayGeneratorMetabo	+	out	output-file			*.tsv,*.traML,*.pqp
AssayGeneratorMetabo	+	out_workspace_directory	string			
AssayGeneratorMetabo	+	precursor_mz_distance	double	1.0e-04		
AssayGeneratorMetabo	+	precursor_rt_tolerance	double	5.0		
AssayGeneratorMetabo	+	preprocessing:feature_only	string	false	true,false	
AssayGeneratorMetabo	+	preprocessing:filter_by_num_masstraces	int	1	1:	
AssayGeneratorMetabo	+	preprocessing:isotope_pattern_iterations	int	3		
AssayGeneratorMetabo	+	preprocessing:no_masstrace_info_isotope_pattern	string	false	true,false	
AssayGeneratorMetabo	+	preprocessing:precursor_mz_tolerance	double	0.005		
AssayGeneratorMetabo	+	preprocessing:precursor_mz_tolerance_unit	string	Da	Da,ppm	
AssayGeneratorMetabo	+	preprocessing:precursor_rt_tolerance	int	5		
AssayGeneratorMetabo	+	sirius:auto_charge	string	false	true,false	
AssayGeneratorMetabo	+	sirius:candidates	int	5	1:	
AssayGeneratorMetabo	+	sirius:compound_timeout	int	10	0:	
AssayGeneratorMetabo	+	sirius:cores	int	1	1:	
AssayGeneratorMetabo	+	sirius:database	string	all	all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda	
AssayGeneratorMetabo	+	sirius:elements	string	CHNOP[5]S[8]Cl[1]		
AssayGeneratorMetabo	+	sirius:ion_tree	string	false	true,false	
AssayGeneratorMetabo	+	sirius:isotope	string	both	score,filter,both,omit	
AssayGeneratorMetabo	+	sirius:most_intense_ms2	string	false	true,false	
AssayGeneratorMetabo	+	sirius:no_recalibration	string	false	true,false	
AssayGeneratorMetabo	+	sirius:noise	int	0	0:	
AssayGeneratorMetabo	+	sirius:ppm_max	int	10		
AssayGeneratorMetabo	+	sirius:profile	string	qtof	qtof,orbitrap,fticr	
AssayGeneratorMetabo	+	sirius:top_n_hits	int	10	1:	
AssayGeneratorMetabo	+	sirius:tree_timeout	int	0	0:	
AssayGeneratorMetabo	+	transition_threshold	double	10.0		
AssayGeneratorMetabo	+	use_exact_mass	string	false	true,false	
AssayGeneratorMetabo	-	filter_by_convex_hulls	int	2
AssayGeneratorMetabo	-	out	output-file			*.tsv
AssayGeneratorMetabo	-	precursor_mz_distance	double	0.0001		
AssayGeneratorMetabo	-	precursor_mz_tolerance	double	0.005		
AssayGeneratorMetabo	-	precursor_mz_tolerance_unit	string	Da	Da,ppm	
AssayGeneratorMetabo	-	precursor_rt_tolerance	double	5		
AssayGeneratorMetabo	-	transition_threshold	double	10		
CometAdapter	+	enzyme	string	Trypsin	unspecific cleavage,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,Arg-C,Trypsin		
CometAdapter	-	enzyme	string	Trypsin	Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage,Trypsin		
CruxAdapter	+	enzyme	string	trypsin	custom-enzyme,chymotrypsin,lys-c,lys-n,trypsin/p,elastase,iodosobenzoate,staph-protease,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,asp-n,trypsin,arg-c,elastase-trypsin-chymotrypsin,no-enzyme	
CruxAdapter	-	enzyme	string	trypsin	custom-enzyme,chymotrypsin,lys-c,lys-n,trypsin/p,elastase,arg-c,iodosobenzoate,staph-protease,proline-endopeptidase,glu-c,pepsin-a,cyanogen-bromide,clostripain,elastase-trypsin-chymotrypsin,no-enzyme,asp-n,trypsin	
DecoyDatabase	+	enzyme	string	Trypsin	Asp-N,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Asp-N/B,Arg-C/P,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
DecoyDatabase	+	type	string	protein	protein,RNA	
DecoyDatabase	-	enzyme	string	Trypsin	leukocyte elastase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N/B,Chymotrypsin/P,Chymotrypsin,V8-DE,V8-E,proline endopeptidase,TrypChymo,Trypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Alpha-lytic protease,glutamyl endopeptidase,Asp-N,Asp-N_ambic,Arg-C/P,Trypsin	
Digestor	+	enzyme	string	Trypsin	Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
Digestor	-	enzyme	string	Trypsin	Trypsin,Arg-C/P,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
DigestorMotif	+	enzyme	string	Trypsin	Trypsin,elastase-trypsin-chymotrypsin,no cleavage,cyanogen-bromide,Clostripain/P,Chymotrypsin,Chymotrypsin/P,CNBr,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,proline-endopeptidase/HKR,staphylococcal protease/D,Glu-C+P,PepsinA + P,unspecific cleavage,Formic_acid,Asp-N/B,Asp-N_ambic,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,proline endopeptidase,leukocyte elastase,Arg-C,Arg-C/P,Asp-N	
DigestorMotif	-	enzyme	string	Trypsin	Arg-C/P,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,elastase-trypsin-chymotrypsin,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,unspecific cleavage,Trypsin	
FalseDiscoveryRate	+	FDR:cleanup:remove_proteins_without_psms	string	true	true,false	
FalseDiscoveryRate	+	FDR:cleanup:remove_psms_without_proteins	string	true	true,false	
FalseDiscoveryRate	+	FDR:cleanup:remove_spectra_without_psms	string	true	true,false	
FalseDiscoveryRate	+	algorithm:conservative	string	true	true,false	
FeatureFinderCentroided	+	algorithm:isotopic_pattern:abundance_12C	double	98.930000000000007	0.0:100.0	
FeatureFinderCentroided	+	algorithm:isotopic_pattern:abundance_14N	double	99.632000000000005	0.0:100.0	
FeatureFinderCentroided	-	algorithm:isotopic_pattern:abundance_12C	double	98.93	0:100	
FeatureFinderCentroided	-	algorithm:isotopic_pattern:abundance_14N	double	99.632	0:100	
FeatureFinderMetabo	+	algorithm:mtd:quant_method	string	area	area,median,max_height	
FeatureFinderMetabo	-	algorithm:mtd:quant_method	string	area	area,median	
FeatureFinderMultiplex	+	out_blacklist	output-file			*.mzML
FeatureLinkerUnlabeledKD	+	algorithm:link:adduct_merging	string	Any	Identical,With_unknown_adducts,Any	
FeatureLinkerUnlabeledKD	+	algorithm:link:charge_merging	string	With_charge_zero	Identical,With_charge_zero,Any	
FeatureLinkerUnlabeledKD	-	algorithm:ignore_adduct	string	true	true,false	
FileConverter	+	NET_executable	input-file			
FileConverter	+	ThermoRaw_executable	input-file	ThermoRawFileParser.exe		*.exe
FileConverter	+	change_im_format	string	none	none,multiple,single	
FileConverter	+	in	input-file			*.mzML,*.mzXML,*.mgf,*.raw,*.cachedMzML,*.mzData,*.dta,*.dta2d,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter	+	in_type	string		mzML,mzXML,mgf,raw,cachedMzML,mzData,dta,dta2d,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta		
FileConverter	+	no_peak_picking	string	false	true,false	
FileConverter	+	out	output-file			*.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv
FileConverter	+	out_type	string		mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv	
FileConverter	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter	-	in_type	string		mzData,mzXML,mzML,cachedMzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta		
FileConverter	-	out	output-file			*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter	-	out_type	string		mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv	
FileFilter	+	peak_options:numpress:float_da	string	none	none,linear,pic,slof	
FileFilter	+	peak_options:numpress:lossy_mass_accuracy	double	-1.0		
FileFilter	+	peak_options:remove_empty	string	false	true,false	
FileFilter	-	peak_options:numpress:intensity_error	double	0.0001		
FileFilter	-	peak_options:numpress:masstime_error	double	0.0001		
FileMerger	+	append_method	string	append_rows	append_rows,append_cols	
HighResPrecursorMassCorrector	+	highest_intensity_peak:mz_tolerance_unit	string	ppm	Da,ppm			
IDFileConverter	+	no_spectra_references_override	string	false	true,false	
IDFilter	+	in_silico_digestion:enzyme	string	Trypsin	staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
IDFilter	+	missed_cleavages:enzyme	string	Trypsin	staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage		
IDFilter	+	precursor:charge	string	:		
IDFilter	+	precursor:length	string	:		
IDFilter	+	remove_duplicate_psm	string	false	true,false	
IDFilter	+	remove_peptide_hits_by_metavalue	string			
IDFilter	+	remove_shared_peptides	string	false	true,false	
IDFilter	-	charge	string	:		
IDFilter	-	in_silico_digestion:enzyme	string	Trypsin	Arg-C,Asp-N/B,Asp-N,Trypsin,Arg-C/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
IDFilter	-	length	string	:		
IDFilter	-	missed_cleavages:enzyme	string	Trypsin	Arg-C,Asp-N/B,Asp-N,Trypsin,Arg-C/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage		
IDFilter	-	thresh:pep	double	0		
IDFilter	-	thresh:prot	double	0		
IDFilter	-	unique	string	false	true,false	
IDFilter	-	unique_per_protein	string	false	true,false	
IDMapper	+	feature:use_centroid_mz	string	true	true,false	
IDMapper	+	mz_reference	string	peptide	precursor,peptide	
IDMapper	-	feature:use_centroid_mz	string	false	true,false	
IDMapper	-	mz_reference	string	precursor	precursor,peptide	
IDMerger	+	merge_proteins_add_PSMs	string	false	true,false	
IDPosteriorErrorProbability	+	fit_algorithm:neg_log_delta	int	6		
ImageCreator	+	mz	string	:		
ImageCreator	+	rt	string	:		
InternalCalibration	+	goodness:MAD	double	2.0		
InternalCalibration	-	goodness:MAD	double	1		
IsobaricAnalyzer	+	tmt16plex:channel_126_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_127C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_127N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_128C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_128N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_129C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_129N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_130C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_130N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_131C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_131N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_132C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_132N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_133C_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_133N_description	string			
IsobaricAnalyzer	+	tmt16plex:channel_134N_description	string			
IsobaricAnalyzer	+	tmt16plex:correction_matrix	string			
IsobaricAnalyzer	+	tmt16plex:reference_channel	string	126	126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C,132N,132C,133N,133C,134N	
IsobaricAnalyzer	+	type	string	itraq4plex	itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt6plex	
IsobaricAnalyzer	-	type	string	itraq4plex	itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt6plex	
LuciphorAdapter	+	rt_tolerance	double	0.01	0.0:	
MRMTransitionGroupPicker	+	algorithm:PeakPickerMRM:write_sn_log_messages	string	false	true,false		
MRMTransitionGroupPicker	-	algorithm:PeakPickerMRM:write_sn_log_messages	string	true	true,false	
MSFraggerAdapter	+	digest:search_enzyme_name	string	Trypsin	Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
MSFraggerAdapter	-	digest:search_enzyme_name	string	Trypsin	Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Trypsin,Arg-C/P,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
MSSimulator	+	algorithm:MSSim:Digestion:enzyme	string	Trypsin	V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo	
MSSimulator	-	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Arg-C/P,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Asp-N/B,Arg-C,Trypsin	
MSstatsConverter	+	method	string	LFQ	LFQ,ISO	
MSstatsConverter	+	msstats_mixture	string	MSstats_Mixture			
MapAlignerIdentification	+	algorithm:min_score	double	0.05		
MapAlignerIdentification	+	algorithm:score_cutoff	string	false	true,false	
MassTraceExtractor	+	algorithm:mtd:quant_method	string	area	area,median,max_height
MassTraceExtractor	-	algorithm:mtd:quant_method	string	area	area,median	
MetaboliteAdductDecharger	+	algorithm:MetaboliteFeatureDeconvolution:mass_max_diff	double	0.05	0.0:	
MetaboliteAdductDecharger	+	algorithm:MetaboliteFeatureDeconvolution:unit	string	Da	Da,ppm	
MetaboliteAdductDecharger	-	algorithm:MetaboliteFeatureDeconvolution:mass_max_diff	double	0.05	
MultiplexResolver	+	algorithm:mz_tolerance	int	10		
MultiplexResolver	+	algorithm:rt_tolerance	int	5		
MultiplexResolver	+	in_blacklist	input-file			*.mzML
MzTabExporter	+	first_run_inference_only	string	false	true,false	
MzTabExporter	+	opt_columns	string		subfeatures
OMSSAAdapter	+	enzyme	string	Trypsin	Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage		
OMSSAAdapter	-	enzyme	string	Trypsin	Arg-C,unspecific cleavage,Asp-N,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,Trypsin,Asp-N_ambic,Chymotrypsin,CNBr		


OpenPepXL	+	decoy_prefix	string	true	true,false	
OpenPepXL	+	decoy_string	string	DECOY_		
OpenPepXL	+	peptide:enzyme	string	Trypsin	Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
OpenPepXL	-	decoy_prefix	string	false	true,false	
OpenPepXL	-	decoy_string	string	decoy		
OpenPepXL	-	peptide:enzyme	string	Trypsin	iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,proline endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Arg-C,Arg-C/P,Trypsin	

OpenPepXLLF	+	decoy_prefix	string	true	true,false	
OpenPepXLLF	+	decoy_string	string	DECOY_		
OpenPepXLLF	+	peptide:enzyme	string	Trypsin	Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,proline-endopeptidase/HKR,Arg-C/P,staphylococcal protease/D,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
OpenPepXLLF	+	algorithm:use_sequence_tags	string	false	true,false
OpenPepXLLF	+	algorithm:sequence_tag_min_length	int	2
OpenPepXLLF	-	algorithm:number_of_scored_candidates	int	10000		
OpenPepXLLF	-	algorithm:pre_scoring	string	false	true,false	
OpenPepXLLF	-	decoy_prefix	string	false	true,false	
OpenPepXLLF	-	decoy_string	string	decoy		
OpenPepXLLF	-	peptide:enzyme	string	Trypsin	Asp-N/B,Asp-N,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Trypsin,Arg-C,Arg-C/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P	
OpenSwathAnalyzer	+	algorithm:Scores:use_ion_mobility_scores	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:im_extra_drift	double	0.0	0.0:	
OpenSwathAnalyzer	+	algorithm:spectrum_addition_method	string	simple	simple,resample	
OpenSwathFileSplitter	+	out_qc	output-file			*.json
OpenSwathRTNormalizer	+	algorithm:Scores:use_ion_mobility_scores	string	false	true,false		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages	string	false	true,false
OpenSwathRTNormalizer	+	algorithm:im_extra_drift	double	0.0	0.0:	
OpenSwathRTNormalizer	+	algorithm:spectrum_addition_method	string	simple	simple,resample			
OpenSwathRTNormalizer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages	string	true	true,false

OpenSwathWorkflow	+	Calibration:debug_im_file	string			
OpenSwathWorkflow	+	Calibration:debug_mz_file	string			
OpenSwathWorkflow	+	Calibration:im_correction_function	string	linear	none,linear	
OpenSwathWorkflow	+	Calibration:ms1_im_calibration	string	false	true,false	
OpenSwathWorkflow	+	Debugging:irt_mzml	output-file			*.mzML
OpenSwathWorkflow	+	Debugging:irt_trafo	output-file			*.trafoXML
OpenSwathWorkflow	+	Scoring:Scores:use_ion_mobility_scores	string	false	true,false		
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:min_peak_width	double	-1.0		
OpenSwathWorkflow	+	Scoring:add_up_spectra	int	1	1:	
OpenSwathWorkflow	+	Scoring:im_extra_drift	double	0.0	0.0:	
OpenSwathWorkflow	+	Scoring:spacing_for_spectra_resampling	double	0.005	0.0:	
OpenSwathWorkflow	+	Scoring:spectrum_addition_method	string	simple	simple,resample	
OpenSwathWorkflow	+	Scoring:stop_report_after_feature	int	5	
OpenSwathWorkflow	+	batchSize	int	250	0:	
OpenSwathWorkflow	+	im_extraction_window_ms1	double	-1.0	
OpenSwathWorkflow	+	irt_im_extraction_window	double	-1.0		
OpenSwathWorkflow	+	irt_mz_extraction_window	double	0.05	0.0:	
OpenSwathWorkflow	+	irt_mz_extraction_window_unit	string	Th	Th,ppm	
OpenSwathWorkflow	+	matching_window_only	string	false	true,false	
OpenSwathWorkflow	+	ms1_isotopes	int	0	0:	
OpenSwathWorkflow	+	mz_correction_function	string	none	none,regression_delta_ppm,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm	
OpenSwathWorkflow	+	mz_extraction_window_ms1	double	0.05	0.0:	
OpenSwathWorkflow	+	mz_extraction_window_ms1_unit	string	Th	ppm,Th	
OpenSwathWorkflow	+	mz_extraction_window_unit	string	Th	Th,ppm	
OpenSwathWorkflow	+	out_qc	output-file			*.json
OpenSwathWorkflow	+	outer_loop_threads	int	-1			
OpenSwathWorkflow	+	tr_irt	input-file			*.traML,*.tsv,*.pqp
OpenSwathWorkflow	+	tr_irt_nonlinear	input-file			*.traML,*.tsv,*.pqp
OpenSwathWorkflow	+	use_ms1_ion_mobility	string	true	true,false	
OpenSwathWorkflow	-	Debugging:irt_mzml	string			
OpenSwathWorkflow	-	Debugging:irt_trafo	string			
OpenSwathWorkflow	-	Scoring:TransitionGroupPicker:min_peak_width	double	14		
OpenSwathWorkflow	-	Scoring:stop_report_after_feature	int	-1	
OpenSwathWorkflow	-	batchSize	int	0	0:	
OpenSwathWorkflow	-	irt_mz_extraction_window	double	0.05	
OpenSwathWorkflow	-	mz_correction_function	string	none	none,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm	
OpenSwathWorkflow	-	ppm	string	false	true,false	
OpenSwathWorkflow	-	ppm_irtwindow	string	false	true,false	
OpenSwathWorkflow	-	tr_irt	input-file			*.traML
PSMFeatureExtractor	+	out_type	string		mzid,idXML	
PeptideIndexer	+	enzyme:name	string	Trypsin	Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,iodosobenzoate,proline endopeptidase,2-iodobenzoate,Alpha-lytic protease,glutamyl endopeptidase	
PeptideIndexer	-	enzyme:name	string	Trypsin	Chymotrypsin/P,Arg-C/P,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin	
PercolatorAdapter	+	enzyme	string	trypsin	no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin,trypsinp	
PercolatorAdapter	-	enzyme	string	trypsin	no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin		
PrecursorIonSelector	+	dt_model	input-file			*.txt
PrecursorIonSelector	+	rt_model	input-file			*.txt
PrecursorIonSelector	+	sim_results	output-file			*.txt
PrecursorIonSelector	-	dt_model	string			
PrecursorIonSelector	-	rt_model	string			
PrecursorIonSelector	-	sim_results	string			
ProteinInference	+	Algorithm:min_peptides_per_protein	int	1	0:	
ProteinInference	+	Algorithm:score_aggregation_method	string	maximum	maximum,product,sum	
ProteinInference	+	Algorithm:skip_count_annotation	string	false		
ProteinInference	+	Algorithm:treat_charge_variants_separately	string	true		
ProteinInference	+	Algorithm:treat_modification_variants_separately	string	true		
ProteinInference	+	Algorithm:use_shared_peptides	string	true		
ProteinInference	+	Merging:annotate_origin	string	true	true,false	
ProteinInference	+	annotate_indist_groups	string	true	true,false	
ProteinInference	+	merge_runs	string	no	no,all	
ProteinInference	-	min_peptides_per_protein	int	2	1:	
ProteinInference	-	treat_charge_variants_separately	string	false	true,false	
ProteinInference	-	treat_modification_variants_separately	string	false	true,false	
ProteinQuantifier	+	best_charge_and_fraction	string	false	true,false	
ProteinQuantifier	+	design	input-file			*.tsv
ProteinQuantifier	+	greedy_group_resolution	string	false	true,false	
ProteinQuantifier	+	mztab	output-file			*.mzTab
ProteinQuantifier	-	filter_charge	string	false	true,false	
RNADigestor	+	cdna	string	false	true,false	
RNADigestor	+	enzyme	string	RNase_T1	RNase_U2,RNase_A,RNase_MC1,RNase_H,no cleavage,unspecific cleavage,RNase_T1,cusativin	
RNADigestor	-	enzyme	string	RNase_T1	unspecific cleavage,no cleavage,RNase_T1	
RNPxlSearch	+	RNPxl:nt_groups	string			
RNPxlSearch	+	RNPxl:only_xl	string	false	true,false	
RNPxlSearch	+	peptide:enzyme	string	Trypsin	Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
RNPxlSearch	-	RNPxl:localization	string	false	true,false	
RNPxlSearch	-	peptide:enzyme	string	Trypsin	Arg-C/P,Asp-N,Chymotrypsin/P,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Trypsin,Arg-C,Asp-N/B,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease	
SimpleSearchEngine	+	Search:enzyme	string	Trypsin	Asp-N/B,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,iodosobenzoate,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
SimpleSearchEngine	+	Search:fragment:mass_tolerance	double	10.0		
SimpleSearchEngine	+	Search:fragment:mass_tolerance_unit	string	ppm	ppm,Da	
SimpleSearchEngine	+	Search:modifications:fixed	string		...	
SimpleSearchEngine	+	Search:modifications:variable	string		...	
SimpleSearchEngine	+	Search:modifications:variable_max_per_peptide	int	2		
SimpleSearchEngine	+	Search:peptide:max_size	int	40		
SimpleSearchEngine	+	Search:peptide:min_size	int	7		
SimpleSearchEngine	+	Search:peptide:missed_cleavages	int	1		
SimpleSearchEngine	+	Search:peptide:motif	string			
SimpleSearchEngine	+	Search:precursor:isotopes	int			
SimpleSearchEngine	+	Search:precursor:mass_tolerance	double	10.0		
SimpleSearchEngine	+	Search:precursor:mass_tolerance_unit	string	ppm	ppm,Da	
SimpleSearchEngine	+	Search:precursor:max_charge	int	5		
SimpleSearchEngine	+	Search:precursor:min_charge	int	2		
SimpleSearchEngine	+	Search:report:top_hits	int	1		
SimpleSearchEngine	-	enzyme	string	Trypsin	Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-N_ambic,Arg-C/P,unspecific cleavage,Arg-C,Asp-N/B,Asp-N,Trypsin	
SimpleSearchEngine	-	fragment:mass_tolerance	double	10		
SimpleSearchEngine	-	fragment:mass_tolerance_unit	string	ppm	ppm,Da	
SimpleSearchEngine	-	modifications:fixed	string		...	
SimpleSearchEngine	-	modifications:variable	string		...	
SimpleSearchEngine	-	modifications:variable_max_per_peptide	int	2		
SimpleSearchEngine	-	peptide:max_size	int	40		
SimpleSearchEngine	-	peptide:min_size	int	7		
SimpleSearchEngine	-	peptide:missed_cleavages	int	1		
SimpleSearchEngine	-	peptide:motif	string			
SimpleSearchEngine	-	precursor:isotopes	int			
SimpleSearchEngine	-	precursor:mass_tolerance	double	10		
SimpleSearchEngine	-	precursor:mass_tolerance_unit	string	ppm	ppm,Da	
SimpleSearchEngine	-	precursor:max_charge	int	5		
SimpleSearchEngine	-	precursor:min_charge	int	2		
SimpleSearchEngine	-	report:top_hits	int	1		
SiriusAdapter	+	converter_mode	string	false	true,false	
SiriusAdapter	+	executable	input-file	sirius		
SiriusAdapter	+	out_ms	output-file			*.ms
SiriusAdapter	+	out_workspace_directory	string			
SiriusAdapter	+	preprocessing:feature_only	string	false	true,false	
SiriusAdapter	+	preprocessing:filter_by_num_masstraces	int	1	1:	
SiriusAdapter	+	preprocessing:isotope_pattern_iterations	int	3		
SiriusAdapter	+	preprocessing:no_masstrace_info_isotope_pattern	string	false	true,false	
SiriusAdapter	+	preprocessing:precursor_mz_tolerance	double	0.005		
SiriusAdapter	+	preprocessing:precursor_mz_tolerance_unit	string	Da	Da,ppm	
SiriusAdapter	+	preprocessing:precursor_rt_tolerance	int	5		
SiriusAdapter	+	sirius:auto_charge	string	false	true,false	
SiriusAdapter	+	sirius:candidates	int	5	1:	
SiriusAdapter	+	sirius:compound_timeout	int	10	0:	
SiriusAdapter	+	sirius:cores	int	1	1:	
SiriusAdapter	+	sirius:database	string	all	all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda	
SiriusAdapter	+	sirius:elements	string	CHNOP[5]S[8]Cl[1]		
SiriusAdapter	+	sirius:ion_tree	string	false	true,false	
SiriusAdapter	+	sirius:isotope	string	both	score,filter,both,omit	
SiriusAdapter	+	sirius:most_intense_ms2	string	false	true,false	
SiriusAdapter	+	sirius:no_recalibration	string	false	true,false	
SiriusAdapter	+	sirius:noise	int	0	0:	
SiriusAdapter	+	sirius:ppm_max	int	10		
SiriusAdapter	+	sirius:profile	string	qtof	qtof,orbitrap,fticr	
SiriusAdapter	+	sirius:top_n_hits	int	10	1:	
SiriusAdapter	+	sirius:tree_timeout	int	0	0:	
SiriusAdapter	-	auto_charge	string	false	true,false	
SiriusAdapter	-	candidates	int	5		
SiriusAdapter	-	compound_timeout	int	10		
SiriusAdapter	-	database	string	all	all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda	
SiriusAdapter	-	elements	string	CHNOP[5]S[8]Cl[1]		
SiriusAdapter	-	executable	input-file			
SiriusAdapter	-	feature_only	string	false	true,false	
SiriusAdapter	-	filter_by_num_masstraces	int	1	1:	
SiriusAdapter	-	ion_tree	string	false	true,false	
SiriusAdapter	-	isotope	string	both	score,filter,both,omit	
SiriusAdapter	-	isotope_pattern_iterations	int	3		
SiriusAdapter	-	most_intense_ms2	string	false	true,false	
SiriusAdapter	-	no_masstrace_info_isotope_pattern	string	false	true,false	
SiriusAdapter	-	no_recalibration	string	false	true,false	
SiriusAdapter	-	noise	int	0		
SiriusAdapter	-	ppm_max	int	10		
SiriusAdapter	-	precursor_mz_tolerance	double	0.005		
SiriusAdapter	-	precursor_mz_tolerance_unit	string	Da	Da,ppm	
SiriusAdapter	-	precursor_rt_tolerance	double	5		
SiriusAdapter	-	profile	string	qtof	qtof,orbitrap,fticr	
SiriusAdapter	-	top_n_hits	int	10		
SiriusAdapter	-	tree_timeout	int	0		
TextExporter	+	id:add_protein_hit_metavalues	int	-1	-1:100	
TextExporter	+	id:protein_groups	string	false	true,false	
XFDR	+	maxborder	double	50.0		
XFDR	+	minborder	double	-50.0		
XFDR	+	minscore	double	-10.0		
XFDR	-	maxborder	int	-1		
XFDR	-	minborder	int	-1		
XFDR	-	minscore	int	0		
XTandemAdapter	+	enzyme	string	Trypsin	Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,Alpha-lytic protease,leukocyte elastase,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,unspecific cleavage	
XTandemAdapter	-	enzyme	string	Trypsin	Arg-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,Arg-C,Trypsin,Asp-N,unspecific cleavage	