Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AssayGeneratorMetabo	+	ambiguity_resolution_mz_tolerance	double	10.0		
AssayGeneratorMetabo	+	ambiguity_resolution_mz_tolerance_unit	string	ppm	ppm,Da	
AssayGeneratorMetabo	+	ambiguity_resolution_rt_tolerance	double	10.0		
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	+	fingerid:candidates	int	10	1:	
AssayGeneratorMetabo	+	fingerid:db	string	BIO		
AssayGeneratorMetabo	+	fragment_annotation_score_threshold	double	0.8	0.0:1.0	
AssayGeneratorMetabo	+	max_transitions	int	6		
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:processors	int	1		
AssayGeneratorMetabo	+	project:q	bool	false		
AssayGeneratorMetabo	+	sirius:candidates_per_ion	int	-1		
AssayGeneratorMetabo	+	sirius:compound_timeout	int	100	0:	
AssayGeneratorMetabo	+	sirius:db	string			
AssayGeneratorMetabo	+	sirius:elements_considered	string			
AssayGeneratorMetabo	+	sirius:elements_enforced	string			
AssayGeneratorMetabo	+	sirius:formula	string			
AssayGeneratorMetabo	+	sirius:ions_considered	string			
AssayGeneratorMetabo	+	sirius:ions_enforced	string			
AssayGeneratorMetabo	+	sirius:no_isotope_filter	bool	false		
AssayGeneratorMetabo	+	sirius:no_isotope_score	bool	false		
AssayGeneratorMetabo	+	sirius:ppm_max	double	10.0		
AssayGeneratorMetabo	+	sirius:ppm_max_ms2	double	10.0		
AssayGeneratorMetabo	+	sirius:profile	string	qtof	default,qtof,orbitrap,fticr	
AssayGeneratorMetabo	+	total_occurrence_filter	double	0.1	0.0:1.0	
AssayGeneratorMetabo	-	max_transitions	int	3		
AssayGeneratorMetabo	-	precursor_rt_tolerance	double	5.0		
AssayGeneratorMetabo	-	preprocessing:precursor_mz_tolerance	double	5.0e-03		
AssayGeneratorMetabo	-	preprocessing:precursor_mz_tolerance_unit	string	Da	Da,ppm	
AssayGeneratorMetabo	-	preprocessing:precursor_rt_tolerance	int	5		
AssayGeneratorMetabo	-	sirius:auto_charge	bool	false		
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	bool	false		
AssayGeneratorMetabo	-	sirius:isotope	string	both	score,filter,both,omit	
AssayGeneratorMetabo	-	sirius:most_intense_ms2	bool	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:	
CometAdapter	+	enzyme	string	Trypsin	Trypsin,Chymotrypsin,Lys-C,Lys-N,Asp-N,CNBr,PepsinA,unspecific cleavage,Trypsin/P,glutamyl endopeptidase,Arg-C	
CometAdapter	+	second_enzyme	string		Trypsin,Chymotrypsin,Lys-C,Lys-N,Asp-N,CNBr,PepsinA,unspecific cleavage,Trypsin/P,glutamyl endopeptidase,Arg-C	
CometAdapter	-	enzyme	string	Trypsin	Arg-C,Trypsin,Asp-N,glutamyl endopeptidase,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P	
CometAdapter	-	second_enzyme	string		Arg-C,Trypsin,Asp-N,glutamyl endopeptidase,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P	
ConsensusID	+	PEPMatrix:matrix	string	PAM30MS	identity,PAM30MS	
ConsensusID	-	PEPMatrix:matrix	string	identity	identity,PAM30MS	
DecoyDatabase	+	enzyme	string	Trypsin	Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Asp-N/B,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,no cleavage,unspecific cleavage,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,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin
DecoyDatabase	-	enzyme	string	Trypsin	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,Trypsin,V8-DE,V8-E,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,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase	
Digestor	+	enzyme	string	Trypsin	glutamyl endopeptidase,Alpha-lytic protease,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,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,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin	
Digestor	-	enzyme	string	Trypsin	Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,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	
DigestorMotif	+	enzyme	string	Trypsin	2-iodobenzoate,iodosobenzoate,Arg-C/P,Asp-N,Asp-N/B,Arg-C,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,glutamyl endopeptidase,Alpha-lytic protease,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Trypsin	
DigestorMotif	-	enzyme	string	Trypsin	cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Trypsin,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P	
FeatureFinderIdentification	+	EMGScoring:init_mom	bool	false		
FeatureFinderIdentification	+	EMGScoring:max_iteration	int	100	1:	
FeatureFinderIdentification	+	extract:batch_size	int	5000	1:	
FeatureFinderIdentification	+	quantify_decoys	bool	false		
FeatureFinderIdentification	+	svm:predictors	string	peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score		
FeatureFinderIdentification	-	extract:batch_size	int	1000	1:	
FeatureFinderIdentification	-	svm:predictors	string	peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score		
FeatureFinderMetaboIdent	+	EMGScoring:init_mom	bool	false		
FeatureFinderMetaboIdent	+	EMGScoring:max_iteration	int	100	1:	
FeatureFinderMetaboIdent	+	debug	int	0	0:	
FeatureFinderMetaboIdent	+	detect:peak_width	double	60.0	0.0:	
FeatureFinderMetaboIdent	-	debug	int	0		
FeatureFinderMetaboIdent	-	detect:peak_width	double	5.0	0.0:	
FeatureLinkerUnlabeledQT	+	algorithm:min_IDscore_forTolCalc	double	1.0		
FeatureLinkerUnlabeledQT	+	algorithm:min_nr_diffs_per_bin	int	50	5:	
FeatureLinkerUnlabeledQT	+	algorithm:noID_penalty	double	0.0	0.0:1.0	
FileConverter	+	change_im_format	string	none	none,concatenated,multiple_spectra,mixed	
FileConverter	+	out	output-file			*.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv,*.sqmass
FileConverter	+	out_type	string		mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv,sqmass	
FileConverter	-	change_im_format	string	none	none,multiple,single	
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	
FileInfo	+	in	input-file			*.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,fid,mzid,trafoXML,fasta,pqp	
FileInfo	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo	-	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp	
GNPSExport	+	merged_spectra:cos_similarity	double	0.9	0.0:	
GNPSExport	+	merged_spectra:precursor_mass_tolerance	double	0.5	0.0:	
GNPSExport	+	ms2_bin_size	double	0.019999999552965	0.0:	
GNPSExport	+	output_type	string	most_intense	merged_spectra,most_intense	
GNPSExport	+	peptide_cutoff	int	5	-1:	
GNPSExport	-	merged_spectra:cos_similarity	double	0.95		
GNPSExport	-	output_type	string	full_spectra	full_spectra,merged_spectra	
GNPSExport	-	precursor_mz_tolerance	double	1.0e-04		
GNPSExport	-	precursor_rt_tolerance	double	5.0		
IDFileConverter	+	fasta_to_mzml:a_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:add_a_ions	bool	false		
IDFileConverter	+	fasta_to_mzml:add_abundant_immonium_ions	bool	false		
IDFileConverter	+	fasta_to_mzml:add_all_precursor_charges	bool	false		
IDFileConverter	+	fasta_to_mzml:add_b_ions	string	true	true,false	
IDFileConverter	+	fasta_to_mzml:add_c_ions	bool	false		
IDFileConverter	+	fasta_to_mzml:add_first_prefix_ion	bool	false		
IDFileConverter	+	fasta_to_mzml:add_losses	bool	false		
IDFileConverter	+	fasta_to_mzml:add_metainfo	bool	false		
IDFileConverter	+	fasta_to_mzml:add_precursor_peaks	bool	false		
IDFileConverter	+	fasta_to_mzml:add_x_ions	bool	false		
IDFileConverter	+	fasta_to_mzml:add_y_ions	string	true	true,false	
IDFileConverter	+	fasta_to_mzml:add_z_ions	bool	false		
IDFileConverter	+	fasta_to_mzml:b_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:c_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:enzyme	string	Trypsin	Arg-C,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,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,no cleavage,unspecific cleavage,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin	
IDFileConverter	+	fasta_to_mzml:isotope_model	string	none	none,coarse,fine	
IDFileConverter	+	fasta_to_mzml:max_charge	int	1		
IDFileConverter	+	fasta_to_mzml:max_isotope	int	2		
IDFileConverter	+	fasta_to_mzml:max_isotope_probability	double	0.05		
IDFileConverter	+	fasta_to_mzml:min_charge	int	1		
IDFileConverter	+	fasta_to_mzml:missed_cleavages	int	0		
IDFileConverter	+	fasta_to_mzml:precursor_H2O_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:precursor_NH3_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:precursor_charge	int	0		
IDFileConverter	+	fasta_to_mzml:precursor_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:relative_loss_intensity	double	0.1		
IDFileConverter	+	fasta_to_mzml:sort_by_position	string	true	true,false	
IDFileConverter	+	fasta_to_mzml:x_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:y_intensity	double	1.0		
IDFileConverter	+	fasta_to_mzml:z_intensity	double	1.0		
IDFileConverter	+	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml,*.fasta
IDFileConverter	+	out	output-file			*.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml,*.mzML
IDFileConverter	+	out_type	string		idXML,mzid,pepXML,FASTA,xquest.xml,mzML	
IDFileConverter	-	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml
IDFileConverter	-	out	output-file			*.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml
IDFileConverter	-	out_type	string		idXML,mzid,pepXML,FASTA,xquest.xml	
IDFilter	+	best:n_spectra	int	0	0:	
IDFilter	+	blacklist:RegEx	string			
IDFilter	+	in_silico_digestion:enzyme	string	Trypsin	Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,no cleavage,unspecific cleavage,Arg-C/P,PepsinA,TrypChymo,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-E,leukocyte elastase,proline endopeptidase,Trypsin/P,V8-DE,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B	
IDFilter	+	missed_cleavages:enzyme	string	Trypsin	Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,no cleavage,unspecific cleavage,Arg-C/P,PepsinA,TrypChymo,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-E,leukocyte elastase,proline endopeptidase,Trypsin/P,V8-DE,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B	
IDFilter	-	in_silico_digestion:enzyme	string	Trypsin	Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N_ambic,Chymotrypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate	
IDFilter	-	missed_cleavages:enzyme	string	Trypsin	Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N_ambic,Chymotrypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate	
MSFraggerAdapter	+	digest:search_enzyme_name	string	Trypsin	PepsinA,TrypChymo,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Lys-N,Lys-C/P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Formic_acid,Lys-C,Arg-C,Arg-C/P,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,no cleavage,unspecific cleavage,Trypsin	
MSFraggerAdapter	+	license	string		yes,no	
MSFraggerAdapter	+	search:localize_delta_mass	int	0	0:	
MSFraggerAdapter	+	tolerance:precursor_mass_tolerance_lower	double	20.0	0.0:	
MSFraggerAdapter	+	tolerance:precursor_mass_tolerance_upper	double	20.0	0.0:	
MSFraggerAdapter	-	digest:search_enzyme_name	string	Trypsin	Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,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	
MSFraggerAdapter	-	tolerance:precursor_mass_tolerance	double	20.0	0.0:	
MSSimulator	+	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Trypsin	
MSSimulator	-	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Trypsin,Arg-C,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,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	
MascotAdapterOnline	+	Mascot_parameters:decoy	bool	false		
MascotAdapterOnline	+	Mascot_server:batch_size	int	50000	0:	
MascotAdapterOnline	-	keep_protein_links	bool	false		
MzTabExporter	+	export_all_psms	bool	false		
NucleicAcidSearchEngine	+	oligo:enzyme	string	no cleavage	RNase_T1,cusativin,RNase_H,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_U2,RNase_A,RNase_MC1	
NucleicAcidSearchEngine	-	oligo:enzyme	string	no cleavage	RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,no cleavage,unspecific cleavage	
OMSSAAdapter	+	enzyme	string	Trypsin	Trypsin,glutamyl endopeptidase,Lys-C/P,no cleavage,unspecific cleavage,CNBr,Formic_acid,Lys-C,Asp-N_ambic,Chymotrypsin,Asp-N,PepsinA,TrypChymo,Trypsin/P,Arg-C	
OMSSAAdapter	-	enzyme	string	Trypsin	Trypsin,CNBr,Formic_acid,Asp-N_ambic,Chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Asp-N,Lys-C,Lys-C/P,Arg-C,PepsinA,TrypChymo,Trypsin/P	
OpenPepXL	+	algorithm:number_top_hits	int	1		
OpenPepXL	+	fragment:mass_tolerance	double	20.0		
OpenPepXL	+	fragment:mass_tolerance_unit	string	ppm	ppm,Da	
OpenPepXL	+	fragment:mass_tolerance_xlinks	double	20.0		
OpenPepXL	+	modifications:variable_max_per_peptide	int	3		
OpenPepXL	+	peptide:enzyme	string	Trypsin	Trypsin,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C/P,PepsinA,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,TrypChymo,Trypsin/P,V8-DE,V8-E,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr	
OpenPepXL	+	peptide:missed_cleavages	int	3		
OpenPepXL	+	precursor:max_charge	int	8		
OpenPepXL	+	precursor:min_charge	int	2		
OpenPepXL	-	algorithm:number_top_hits	int	5		
OpenPepXL	-	fragment:mass_tolerance	double	0.2		
OpenPepXL	-	fragment:mass_tolerance_unit	string	Da	ppm,Da	
OpenPepXL	-	fragment:mass_tolerance_xlinks	double	0.3		
OpenPepXL	-	modifications:variable_max_per_peptide	int	2		
OpenPepXL	-	peptide:enzyme	string	Trypsin	Trypsin,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic	
OpenPepXL	-	peptide:missed_cleavages	int	2		
OpenPepXL	-	precursor:max_charge	int	7		
OpenPepXL	-	precursor:min_charge	int	3		
OpenPepXLLF	+	algorithm:number_top_hits	int	1		
OpenPepXLLF	+	modifications:variable_max_per_peptide	int	3		
OpenPepXLLF	+	peptide:enzyme	string	Trypsin	Trypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage,Arg-C,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin	
OpenPepXLLF	+	peptide:missed_cleavages	int	3		
OpenPepXLLF	+	precursor:max_charge	int	8		
OpenPepXLLF	+	precursor:min_charge	int	2		
OpenPepXLLF	-	algorithm:number_top_hits	int	5		
OpenPepXLLF	-	modifications:variable_max_per_peptide	int	2		
OpenPepXLLF	-	peptide:enzyme	string	Trypsin	Trypsin,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic	
OpenPepXLLF	-	peptide:missed_cleavages	int	2		
OpenPepXLLF	-	precursor:max_charge	int	7		
OpenPepXLLF	-	precursor:min_charge	int	3		
OpenSwathAnalyzer	+	algorithm:EMGScoring:init_mom	bool	false		
OpenSwathAnalyzer	+	algorithm:Scores:use_ionseries_scores	string	true	true,false	
OpenSwathAnalyzer	+	algorithm:Scores:use_ms2_isotope_scores	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:EMGScoring:init_mom	bool	false		
OpenSwathRTNormalizer	+	algorithm:Scores:use_ionseries_scores	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_ms2_isotope_scores	string	true	true,false	
OpenSwathWorkflow	+	Scoring:EMGScoring:init_mom	bool	false		
OpenSwathWorkflow	+	Scoring:Scores:use_ionseries_scores	string	true	true,false	
OpenSwathWorkflow	+	Scoring:Scores:use_ms2_isotope_scores	string	true	true,false	
PeptideIndexer	+	enzyme:name	string	auto	auto,Lys-N,Lys-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C,Arg-C/P,Asp-N,Formic_acid,Lys-C,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,PepsinA,TrypChymo,Trypsin/P,V8-DE,Trypsin	
PeptideIndexer	-	enzyme:name	string	auto	auto,Asp-N,Asp-N/B,Asp-N_ambic,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,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,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid	
PercolatorAdapter	+	osw_level	string	ms2	ms1,ms2,transition	
PercolatorAdapter	-	osw_level	string	ms2		
ProteomicsLFQ	+	Alignment:align_algorithm:max_rt_shift	double	0.1	0.0:	
ProteomicsLFQ	+	Alignment:align_algorithm:min_run_occur	int	2	2:	
ProteomicsLFQ	+	Alignment:align_algorithm:min_score	double	0.05		
ProteomicsLFQ	+	Alignment:align_algorithm:score_cutoff	bool	false		
ProteomicsLFQ	+	Alignment:align_algorithm:use_feature_rt	string	true	true,false	
ProteomicsLFQ	+	Alignment:align_algorithm:use_unassigned_peptides	bool	false		
ProteomicsLFQ	+	Alignment:model:b_spline:boundary_condition	int	2	0:2	
ProteomicsLFQ	+	Alignment:model:b_spline:extrapolate	string	linear	linear,b_spline,constant,global_linear	
ProteomicsLFQ	+	Alignment:model:b_spline:num_nodes	int	5	0:	
ProteomicsLFQ	+	Alignment:model:b_spline:wavelength	double	0.0	0.0:	
ProteomicsLFQ	+	Alignment:model:interpolated:extrapolation_type	string	two-point-linear	two-point-linear,four-point-linear,global-linear	
ProteomicsLFQ	+	Alignment:model:interpolated:interpolation_type	string	cspline	linear,cspline,akima	
ProteomicsLFQ	+	Alignment:model:linear:symmetric_regression	bool	false		
ProteomicsLFQ	+	Alignment:model:linear:x_datum_max	double	1.0e15		
ProteomicsLFQ	+	Alignment:model:linear:x_datum_min	double	1.0e-15		
ProteomicsLFQ	+	Alignment:model:linear:x_weight	string		1/x,1/x2,ln(x),	
ProteomicsLFQ	+	Alignment:model:linear:y_datum_max	double	1.0e15		
ProteomicsLFQ	+	Alignment:model:linear:y_datum_min	double	1.0e-15		
ProteomicsLFQ	+	Alignment:model:linear:y_weight	string		1/y,1/y2,ln(y),	
ProteomicsLFQ	+	Alignment:model:lowess:delta	double	-1.0		
ProteomicsLFQ	+	Alignment:model:lowess:extrapolation_type	string	four-point-linear	two-point-linear,four-point-linear,global-linear	
ProteomicsLFQ	+	Alignment:model:lowess:interpolation_type	string	cspline	linear,cspline,akima	
ProteomicsLFQ	+	Alignment:model:lowess:num_iterations	int	3	0:	
ProteomicsLFQ	+	Alignment:model:lowess:span	double	0.666666666666667	0.0:1.0	
ProteomicsLFQ	+	Alignment:model:type	string	b_spline	linear,b_spline,lowess,interpolated	
ProteomicsLFQ	+	Alignment:model_type	string	b_spline	linear,b_spline,lowess,interpolated	
ProteomicsLFQ	+	Linking:min_IDscore_forTolCalc	double	1.0		
ProteomicsLFQ	+	Linking:min_nr_diffs_per_bin	int	50	5:	
ProteomicsLFQ	+	Linking:noID_penalty	double	0.0	0.0:1.0	
ProteomicsLFQ	+	PeptideQuantification:EMGScoring:init_mom	bool	false		
ProteomicsLFQ	+	PeptideQuantification:EMGScoring:max_iteration	int	100	1:	
ProteomicsLFQ	+	PeptideQuantification:extract:batch_size	int	5000	1:	
ProteomicsLFQ	+	PeptideQuantification:quantify_decoys	bool	false		
ProteomicsLFQ	+	PeptideQuantification:svm:predictors	string	peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score		
ProteomicsLFQ	+	Seeding:charge	string	2:5		
ProteomicsLFQ	+	Seeding:intThreshold	double	1.0e04		
ProteomicsLFQ	+	Seeding:traceRTTolerance	double	3.0		
ProteomicsLFQ	+	alignment_order	string	star	star,treeguided	
ProteomicsLFQ	+	out_triqler	output-file			*.tsv
ProteomicsLFQ	-	Alignment:max_rt_shift	double	0.1	0.0:	
ProteomicsLFQ	-	Alignment:min_run_occur	int	2	2:	
ProteomicsLFQ	-	Alignment:min_score	double	0.05		
ProteomicsLFQ	-	Alignment:score_cutoff	bool	false		
ProteomicsLFQ	-	Alignment:use_feature_rt	string	true	true,false	
ProteomicsLFQ	-	Alignment:use_unassigned_peptides	bool	false		
ProteomicsLFQ	-	PeptideQuantification:extract:batch_size	int	1000	1:	
ProteomicsLFQ	-	PeptideQuantification:svm:predictors	string	peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score		
ProteomicsLFQ	-	seedThreshold	double	1.0e04		
QCCalculator	+	address	string			
QCCalculator	+	description	string			
QCCalculator	+	label	string	label		
QCCalculator	+	name	string			
QCCalculator	+	out	output-file			*.mzQC,*.qcML
QCCalculator	+	out_type	string		mzQC,qcML	
QCCalculator	-	out	output-file			*.qcML
QualityControl	+	out_evd	string			
RNADigestor	+	enzyme	string	RNase_T1	RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,mazF,colicin_E5,no cleavage,unspecific cleavage	
RNADigestor	-	enzyme	string	RNase_T1	RNase_T1,RNase_MC1,RNase_H,no cleavage,unspecific cleavage,cusativin,RNase_U2,RNase_A	
RNPxlSearch	+	peptide:enzyme	string	Trypsin	PepsinA,TrypChymo,Trypsin/P,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C/P,Lys-C,Lys-N,Lys-C/P,Arg-C,V8-DE,V8-E,leukocyte elastase,proline endopeptidase	
RNPxlSearch	-	peptide:enzyme	string	Trypsin	proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,no cleavage,unspecific cleavage,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR	
SimpleSearchEngine	+	Search:annotate:PSM	string		ALL,fragment_mz_error_median_ppm,precursor_mz_error_ppm,matched_prefix_ions_fraction,matched_suffix_ions_fraction	
SimpleSearchEngine	+	Search:enzyme	string	Trypsin	Trypsin,Lys-C/P,PepsinA,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,Lys-N,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C/P,TrypChymo,Trypsin/P	
SimpleSearchEngine	-	Search:annotate:PSM	string		fragment_mz_error_median_ppm,precursor_mz_error_ppm	
SimpleSearchEngine	-	Search:enzyme	string	Trypsin	Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,TrypChymo,Arg-C/P,Arg-C,unspecific cleavage,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Lys-C,Lys-N,Chymotrypsin/P,CNBr,Formic_acid	
SiriusAdapter	+	fingerid:candidates	int	10	1:	
SiriusAdapter	+	fingerid:db	string	BIO		
SiriusAdapter	+	out_project_space	string			
SiriusAdapter	+	preprocessing:precursor_mz_tolerance	double	10.0		
SiriusAdapter	+	preprocessing:precursor_mz_tolerance_unit	string	ppm	Da,ppm	
SiriusAdapter	+	preprocessing:precursor_rt_tolerance	double	5.0		
SiriusAdapter	+	project:ignore_formula	bool	false		
SiriusAdapter	+	project:processors	int	1		
SiriusAdapter	+	project:q	bool	false		
SiriusAdapter	+	sirius:candidates_per_ion	int	-1		
SiriusAdapter	+	sirius:compound_timeout	int	100	0:	
SiriusAdapter	+	sirius:db	string			
SiriusAdapter	+	sirius:elements_considered	string			
SiriusAdapter	+	sirius:elements_enforced	string			
SiriusAdapter	+	sirius:formula	string			
SiriusAdapter	+	sirius:ions_considered	string			
SiriusAdapter	+	sirius:ions_enforced	string			
SiriusAdapter	+	sirius:no_isotope_filter	bool	false		
SiriusAdapter	+	sirius:no_isotope_score	bool	false		
SiriusAdapter	+	sirius:ppm_max	double	10.0		
SiriusAdapter	+	sirius:ppm_max_ms2	double	10.0		
SiriusAdapter	+	sirius:profile	string	qtof	default,qtof,orbitrap,fticr	
SiriusAdapter	-	out_workspace_directory	string			
SiriusAdapter	-	preprocessing:precursor_mz_tolerance	double	5.0e-03		
SiriusAdapter	-	preprocessing:precursor_mz_tolerance_unit	string	Da	Da,ppm	
SiriusAdapter	-	preprocessing:precursor_rt_tolerance	int	5		
SiriusAdapter	-	sirius:auto_charge	bool	false		
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	bool	false		
SiriusAdapter	-	sirius:isotope	string	both	score,filter,both,omit	
SiriusAdapter	-	sirius:most_intense_ms2	bool	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:	
SpectraMerger	+	algorithm:sort_blocks	string	RT_ascending	RT_ascending,RT_descending	
SpectraMerger	-	algorithm:sort_blocks	string	RT_ascending	RT_ascending, RT_descending	
TextExporter	+	out	output-file			*.tsv,*.csv,*.txt
TextExporter	+	out_type	string		tsv,csv,txt	
TextExporter	-	out	output-file			*.tsv
TextExporter	-	separator	string			
XTandemAdapter	+	enzyme	string	Trypsin	PepsinA,TrypChymo,Trypsin/P,Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,unspecific cleavage,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Lys-C,Lys-N,Lys-C/P,Arg-C,V8-DE,V8-E,leukocyte elastase	
XTandemAdapter	-	enzyme	string	Trypsin	Asp-N_ambic,Chymotrypsin,Trypsin,Formic_acid,Lys-C,Alpha-lytic protease,2-iodobenzoate,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Chymotrypsin/P,CNBr,Arg-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase	
