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CHANGELOG_PARAMS
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268 lines (260 loc) · 33.8 KB
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- ADDED:
- FeatureFinderLFQ -- Feature detection for LC-MS1 data (EXPERIMENTAL)
- IsobaricWorkflow -- Calculates isobaric quantitative values for peptides
- OpenNuXL -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra
- PeakPickerIM -- Applies PeakPickerIM to an mzML file
- PeptideDataBaseSearchFI -- Annotates bottom-up MS/MS spectra using PeptideDataBaseSearchFI
- QPXConverter -- Converts IdXML files to parquet format following QPX PSM specification
- REMOVED:
- IDMassAccuracy -- Calculates a distribution of the mass error from given mass spectra and IDs
- OpenPepXLLF -- Protein-protein cross linking with label-free linkers
- SpecLibCreator -- Creates an MSP formatted spectral library
- SpecLibSearcher -- Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library
- CHANGED PARAMETERS:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
CometAdapter + enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,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
CometAdapter - enzyme string Trypsin Lys-C,Lys-N,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Trypsin,Arg-C,unspecific cleavage,Lys-C/P,PepsinA,Trypsin/P,leukocyte elastase,glutamyl endopeptidase,no cleavage
CometAdapter + PeptideIndexing:enzyme:name string auto auto,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Trypsin,Formic_acid,Lys-C,Lys-N,Lys-C/P,Arg-C,Arg-C/P,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,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B
CometAdapter - PeptideIndexing:enzyme:name string auto auto,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C,Lys-N,Lys-C/P,PepsinA,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic
CometAdapter + second_enzyme string Arg-C/P,Asp-N,Asp-N/B,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,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
CometAdapter - second_enzyme string Lys-C,Lys-N,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Trypsin,Arg-C,unspecific cleavage,Lys-C/P,PepsinA,Trypsin/P,leukocyte elastase,glutamyl endopeptidase,no cleavage
DecoyDatabase + enzyme string Trypsin Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,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,glutamyl endopeptidase,Alpha-lytic protease,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P
DecoyDatabase - enzyme string Trypsin Lys-C,Lys-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,proline-endopeptidase/HKR,Glu-C+P,Trypsin,Arg-C,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,no cleavage,unspecific cleavage
DecoyDatabase + shuffle_decoy_ratio int 1 1:
Digestor + enzyme string Trypsin Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,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,Alpha-lytic protease,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P
Digestor - enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,no cleavage,unspecific cleavage,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DigestorMotif + enzyme string Trypsin Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,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
DigestorMotif - enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,no cleavage,unspecific cleavage,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
Digestor + replace_ambiguous 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,PEP,Posterior Error Probability,pep,posterior_error_probability,FDR,false discovery rate,fdr,MS:1001491,q-Value,q-value,qval,qvalue
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
FeatureFinderCentroided + faims_merge_features string true true,false
FeatureFinderIdentification + extract:IM_window double 0.06 0.0:
FeatureFinderIdentification + faims:merge_features string true true,false
FeatureFinderMetabo + algorithm:mtd:ion_mobility_tolerance double 0.01
FeatureFinderMetabo + faims_merge_features string true true,false
FeatureFinderMetaboIdent + extract:im_window double 0.0 0.0:
FeatureFinderMetaboIdent + faims:merge_features string true true,false
FeatureFinderMultiplex + faims_merge_features string true true,false
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_k_folds int 5 2:
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_metric string mae p90,p95,p99,rmse,mae
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_min_neighbors int 5 3:
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_span bool false
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_span_grid string
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_span_max double 0.8 :0.99
FeatureLinkerUnlabeledKD + algorithm:LOWESS:auto_span_min double 0.15 1.0e-03:
FileFilter + peak_options:remove_metadataarrays bool false
FileFilter + rt_block_mode string as_is as_is,extend_to_preserve_full_cycle,shrink_to_preserve_full_cycle
FLASHDeconv - Algorithm:allowed_isotope_error int 1
FLASHDeconv - Algorithm:isolation_window double 5.0
FLASHDeconv - Algorithm:max_charge int 100
FLASHDeconv - Algorithm:max_mass double 1.0e05
FLASHDeconv - Algorithm:max_mz double -1.0
FLASHDeconv - Algorithm:max_rt double -1.0
FLASHDeconv - Algorithm:min_charge int 1
FLASHDeconv - Algorithm:min_intensity double 0.0
FLASHDeconv - Algorithm:min_isotope_cosine double
FLASHDeconv - Algorithm:min_mass double 50.0
FLASHDeconv - Algorithm:min_mz double -1.0
FLASHDeconv - Algorithm:min_rt double -1.0
FLASHDeconv - Algorithm:tol double
FLASHDeconv + FD:allowed_isotope_error int 0
FLASHDeconv + FD:ida_log string
FLASHDeconv + FD:isolation_window double 5.0
FLASHDeconv + FD:merging_max_ms_level int 2 1:
FLASHDeconv + FD:merging_method int 0 0:2
FLASHDeconv + FD:merging_min_ms_level int 1 1:
FLASHDeconv + FD:precursor_MS1_window int 1 1:
FLASHDeconv + FD:report_FDR bool false
FLASHDeconv + FD:use_RNA_averagine bool false
FLASHDeconv - FeatureTracing:mass_error_ppm double -1.0
FLASHDeconv - FeatureTracing:max_trace_length double -1.0
FLASHDeconv - FeatureTracing:min_isotope_cosine double -1.0
FLASHDeconv - FeatureTracing:min_sample_rate double 0.05
FLASHDeconv - FeatureTracing:min_trace_length double 10.0
FLASHDeconv - FeatureTracing:quant_method string area area,median,max_height
FLASHDeconv - forced_MS_level int 0 0:
FLASHDeconv + ft:ion_mobility_tolerance double 0.01
FLASHDeconv + ft:mass_error_ppm double -1.0
FLASHDeconv + ft:max_trace_length double -1.0
FLASHDeconv + ft:min_cos double -1.0
FLASHDeconv + ft:min_sample_rate double 0.1
FLASHDeconv + ft:min_trace_length double 10.0
FLASHDeconv + ft:quant_method string area area,median,max_height
FLASHDeconv - in_log string
FLASHDeconv + iq:isotope_correction string true true,false
FLASHDeconv + iq:only_fully_quantified bool false
FLASHDeconv + iq:reporter_mz_tol double 2.0e-03
FLASHDeconv + iq:type string none none,itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt18plex,tmt6plex
FLASHDeconv + keep_empty_out bool false
FLASHDeconv + max_ms_level int -1
FLASHDeconv - max_MS_level int 3 1:
FLASHDeconv + max_mz double -1.0
FLASHDeconv + max_rt double -1.0
FLASHDeconv - merging_method int 0 0:2
FLASHDeconv + min_mz double -1.0
FLASHDeconv - min_precursor_snr double 1.0
FLASHDeconv + min_rt double -1.0
FLASHDeconv + out_feature1 output-file *.feature
FLASHDeconv + out_feature2 output-file *.feature
FLASHDeconv + out_msalign1 output-file *.msalign
FLASHDeconv + out_msalign2 output-file *.msalign
FLASHDeconv - out_promex output-file *.ms1ft
FLASHDeconv + out_quant output-file *.tsv
FLASHDeconv + out_spec1 output-file *.tsv
FLASHDeconv + out_spec2 output-file *.tsv
FLASHDeconv + out_spec3 output-file *.tsv
FLASHDeconv + out_spec4 output-file *.tsv
FLASHDeconv - out_spec output-file *.tsv
FLASHDeconv - out_topFD_feature output-file *.feature
FLASHDeconv - out_topFD output-file *.msalign
FLASHDeconv - preceding_MS1_count int 3 1:
FLASHDeconv - report_FDR int 0 0:1
FLASHDeconv + SD:max_charge int 100
FLASHDeconv + SD:max_mass double 1.0e05
FLASHDeconv + SD:min_charge int 1
FLASHDeconv + SD:min_cos double 0.5:1.0
FLASHDeconv + SD:min_mass double 50.0
FLASHDeconv + SD:min_snr double 0.25:
FLASHDeconv + SD:precursor_charge int 0 0:
FLASHDeconv + SD:precursor_mz double 0.0 0.0:
FLASHDeconv + SD:tol double
FLASHDeconv - target_precursor_charge int 0
FLASHDeconv - target_precursor_mz double 0.0
FLASHDeconv - use_RNA_averagine int 0 0:1
FLASHDeconv + write_detail bool false
FLASHDeconv - write_detail int 0 0:1
IDFileConverter + fasta_to_mzml:add_internal_fragments bool false
IDFileConverter + fasta_to_mzml:add_term_losses bool false
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Arg-C,Arg-C/P,Asp-N,Trypsin,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,leukocyte elastase,proline endopeptidase,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,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
IDFileConverter - fasta_to_mzml:enzyme string Trypsin Arg-C,Arg-C/P,Asp-N,Trypsin,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,proline endopeptidase,glutamyl endopeptidase,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,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D
IDFilter + in_silico_digestion:enzyme string Trypsin iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Asp-N,Asp-N/B,Arg-C,Arg-C/P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Formic_acid,Lys-C,Lys-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Trypsin,Lys-C/P,PepsinA,TrypChymo
IDFilter - in_silico_digestion:enzyme string Trypsin no cleavage,unspecific cleavage,PepsinA,TrypChymo,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Formic_acid,Lys-C,Lys-N,Lys-C/P,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C,Arg-C/P
IDFilter + missed_cleavages:enzyme string Trypsin iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Asp-N,Asp-N/B,Arg-C,Arg-C/P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Formic_acid,Lys-C,Lys-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Trypsin,Lys-C/P,PepsinA,TrypChymo
IDFilter - missed_cleavages:enzyme string Trypsin no cleavage,unspecific cleavage,PepsinA,TrypChymo,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,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Formic_acid,Lys-C,Lys-N,Lys-C/P,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C,Arg-C/P
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,PEP,Posterior Error Probability,pep,posterior_error_probability,FDR,false discovery rate,fdr,MS:1001491,q-Value,q-value,qval,qvalue
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,PEP,Posterior Error Probability,pep,posterior_error_probability,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
IDSplitter + in input-file *.featureXML,*.consensusXML
IDSplitter - in input-file *.mzML,*.featureXML,*.consensusXML
IDSplitter + out output-file *.featureXML,*.consensusXML
IDSplitter - out output-file *.mzML,*.featureXML,*.consensusXML
MapAlignerIdentification + model:lowess:auto_k_folds int 5 2:
MapAlignerIdentification + model:lowess:auto_metric string mae p90,p95,p99,rmse,mae
MapAlignerIdentification + model:lowess:auto_min_neighbors int 5 3:
MapAlignerIdentification + model:lowess:auto_span bool false
MapAlignerIdentification + model:lowess:auto_span_grid string
MapAlignerIdentification + model:lowess:auto_span_max double 0.8 :0.99
MapAlignerIdentification + model:lowess:auto_span_min double 0.15 1.0e-03:
MapAlignerTreeGuided + algorithm:model:lowess:auto_k_folds int 5 2:
MapAlignerTreeGuided + algorithm:model:lowess:auto_metric string mae p90,p95,p99,rmse,mae
MapAlignerTreeGuided + algorithm:model:lowess:auto_min_neighbors int 5 3:
MapAlignerTreeGuided + algorithm:model:lowess:auto_span bool false
MapAlignerTreeGuided + algorithm:model:lowess:auto_span_grid string
MapAlignerTreeGuided + algorithm:model:lowess:auto_span_max double 0.8 :0.99
MapAlignerTreeGuided + algorithm:model:lowess:auto_span_min double 0.15 1.0e-03:
MapRTTransformer + model:lowess:auto_k_folds int 5 2:
MapRTTransformer + model:lowess:auto_metric string mae p90,p95,p99,rmse,mae
MapRTTransformer + model:lowess:auto_min_neighbors int 5 3:
MapRTTransformer + model:lowess:auto_span bool false
MapRTTransformer + model:lowess:auto_span_grid string
MapRTTransformer + model:lowess:auto_span_max double 0.8 :0.99
MapRTTransformer + model:lowess:auto_span_min double 0.15 1.0e-03:
MassTraceExtractor + algorithm:mtd:ion_mobility_tolerance double 0.01
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,Arg-C,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide
MSFraggerAdapter + digest:search_enzyme_name string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Trypsin,Arg-C,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P
MSFraggerAdapter + PeptideIndexing:enzyme:name string auto auto,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Asp-N/B,TrypChymo,Trypsin/P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
MSFraggerAdapter - PeptideIndexing:enzyme:name string auto auto,Lys-C/P,PepsinA,Arg-C,Arg-C/P,Asp-N,V8-DE,V8-E,leukocyte elastase,Formic_acid,Lys-C,Lys-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,TrypChymo,Trypsin/P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Trypsin
MSGFPlusAdapter + PeptideIndexing:enzyme:name string auto auto,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Trypsin,Arg-C,Arg-C/P,Asp-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,TrypChymo,Trypsin/P
MSGFPlusAdapter - PeptideIndexing:enzyme:name string auto auto,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Trypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,Asp-N,Asp-N/B,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P
NucleicAcidSearchEngine + modifications:fixed string io6A,s2U,k2C,m2Gm,Ym,f5Cm,Qbase,ac4Cm,imG-14,cm5s2U,mnm5s2U,m227G,yW-58,I,g6A,nm5U,m7G,s2Um,Y,hm5C,m5U,preQ0,o2yW,m5Um,preQ1,m66Am,ac6A,ms2io6A,Am,Im,mnm5U,m22G,t6A,m8A,m7GpppN,m27GpppN,m227GpppN,mpppN,m28A,acp3D,acp3Y,imG,D,N,C+,m27Gm,ho5C,inm5U,inm5Um,inm5s2U,pppN,GpppN,CoApN,m44C,acCoApN,malonyl-CoApN,succinyl-CoApN,ppN,NADpN,m6t6A,OHyWy,pG(pN),ncm5s2U,nchm5U,mchm5Um,pN,ges2U,cmnm5ges2U,mnm5ges2U,nm5ges2U,m5D,mmpN,mpN,5'-OH-N,N2'3'cp,ct6A,hm6A,f6A,cnm5U,mcmo5Um,m5C,ms2ct6A,ht6A,msms2i6A,hm5Cm,pY,pm5C,ps2U,hn6A,pD,pm2G,pm66A,pGm,pm5U,pm22G,pm3U,m5Cm,Ar(p),pac4C,pCm,pppG,pm7G,pm1A,pUm,pAm,pm4Cm,pC2'3'cp,tm5U,pm6A,pyW,pm1G,pA2'3'cp,ps4U,pI,ppG,pm2A,m1G,pmcm5s2U,cmnm5Um,pse2U,pt6A,pf5C,pppA,pG,pG2'3'cp,pms2i6A,pcmo5U,pyW,Xm,pm44C,pi6A,phm5C,pU,pAr(p),pac4Cm,pGp,m1I,pU2'3'cp,mcm5U,Gm,pm4C,ncm5Um,pm5Um,pmnm5U,pm3C,m5s2U,yW,pC,pm6t6A,f5C,pAp,m1Am,m1Im,ApppN,AppppN,ApppppN,m6ApppN,m6AppppN,m6ApppppN,m7GppppN,Gr(p),pm1Am,pm1Gm,pm1Im,pm1acp3Y,pm1I,pm1Y,pk2C,ps2C,pm1acp3Y,pm3Y,nm5s2U,pm5Cm,pmchm5U,pinm5Um,pinm5s2U,pinm5U,pnm5U,pncm5U,pchm5U,pcmnm5U,pcm5U,m2G,pho5U,pmcm5Um,pmcm5U,pmo5U,pm5D,pmimG,phm5Cm,pIm,pYm,pmcmo5Um,m2A,pGr(p),pm28A,pmsms2i6A,pges2U,pms2ct6A,pms2io6A,pms2hn6A,pms2m6A,pms2t6A,ps2Um,pm3Um,pacp3D,pacp3U,pimG-14,pmchm5Um,pnm5ges2U,pnm5se2U,pnm5s2U,pnchm5U,pncm5Um,m4Cm,pncm5s2U,pcm5s2U,pcmnm5Um,pcmnm5ges2U,pcmnm5se2U,pcmnm5s2U,pcnm5U,pf5Cm,pho5C,pm5s2U,m27G,m22Gm,pmnm5ges2U,pmnm5se2U,pmnm5s2U,ptm5s2U,ptm5U,pyW-86,pyW-72,pyW-58,ppreQ1,ppreQ0,m66A,pm8A,pC+,pG+,pct6A,poQ,pgalQ,pgluQ,pht6A,pOHyW,pimG2,gluQ,pmanQ,pOHyWy,pm27Gm,pQ,pOHyWx,pmcmo5U,pimG,pm44Cm,pm2Gm,pm22Gm,ncm5U,pm6Am,pm66Am,pio6A,pac6A,pf6A,pg6A,phm6A,phn6A,cm5U,pm27G,pm227G,pm27Gm,pA,cmnm5s2U,cmo5U,m3Y,m3U,ms2m6A,Um,ms2i6A,m3C,cmnm5se2U,ms2t6A,i6A,m3Um,mcmo5U,mimG,oQ,preQ1base,nm5se2U,m1Gm,ho5U,Q,xG,mcm5s2U,m44Cm,s4U,xC,yW-86,xA,chm5U,mo5U,acp3U,xU,yW-72,mnm5se2U,ms2hn6A,m1acp3Y,mcm5Um,ac4C,m6Am,m1A,Cm,mchm5U,galQ,cmnm5U,m1Y,imG2,m4C,manQ,tm5s2U,s2C,OHyWx,se2U,preQ0base,m6A,OHyW,xX,G+,3'-p,5'-p,5'-p*,3'-c,mA,mC,mG,mU,sU,mmA,mAm,mCm,mGm,mUm,cmo5U/chm5U,mchm5U/mcmo5U,mchm5Um/mcmo5Um,m6t6A/hn6A,galQ/manQ,mA?,mC?,mG?,mU?,mI?,msU?,mmA?,mmC?,mmG?,mmmG?,ac4C/f5Cm?,acp3U/cmnm5Um?,dA,dC,dG,dU,dT,A*,C*,G*,U*,dA*,dC*,dG*,dU*,dT*
NucleicAcidSearchEngine - oligo:enzyme string no cleavage cusativin,RNase_T1_Phosphatase,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_T1,RNase_MC1,RNase_H,RNase_4,RNase_4p,RNase_4c,RNase_U2,RNase_A
NucleicAcidSearchEngine + oligo:enzyme string no cleavage RNase_T1,cusativin,RNase_U2,RNase_4,RNase_4p,RNase_4c,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_A,RNase_MC1,RNase_H,RNase_T1_Phosphatase
OpenPepXL - peptide:enzyme string Trypsin PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Trypsin,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Formic_acid,Lys-C,Lys-N,Lys-C/P,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P
OpenPepXL + peptide:enzyme string Trypsin Trypsin,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Arg-C,Arg-C/P,Asp-N,PepsinA,TrypChymo,Trypsin/P,V8-DE
OpenSwathWorkflow + auto_irt 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:irt_bins int 100 5:
OpenSwathWorkflow + Calibration:irt_bins_nonlinear int 2000 5:
OpenSwathWorkflow + Calibration:irt_peptides_per_bin int 5 1:
OpenSwathWorkflow + Calibration:irt_peptides_per_bin_nonlinear int 50 0:
OpenSwathWorkflow + Calibration:irt_seed int 5489 0:
OpenSwathWorkflow + Calibration:MassIMCorrection:debug_im_file string
OpenSwathWorkflow + Calibration:MassIMCorrection:debug_mz_file string
OpenSwathWorkflow + Calibration:MassIMCorrection:im_correction_function string linear none,linear
OpenSwathWorkflow + Calibration:MassIMCorrection:im_estimation_padding_factor double 1.3 1.0:
OpenSwathWorkflow + Calibration:MassIMCorrection:im_extraction_window double -1.0
OpenSwathWorkflow + Calibration:MassIMCorrection:ms1_im_calibration bool false
OpenSwathWorkflow + Calibration:MassIMCorrection: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 + Calibration:MassIMCorrection:mz_estimation_padding_factor double 1.3 1.0:
OpenSwathWorkflow + Calibration:MassIMCorrection:mz_extraction_window double -1.0
OpenSwathWorkflow + Calibration:MassIMCorrection:mz_extraction_window_ppm bool false
OpenSwathWorkflow - Calibration:ms1_im_calibration bool false
OpenSwathWorkflow + Calibration:RTNormalization:alignmentMethod string linear linear,interpolated,lowess,b_spline
OpenSwathWorkflow + Calibration:RTNormalization:b_spline:num_nodes int 5 0:
OpenSwathWorkflow + Calibration:RTNormalization:estimateBestPeptides bool false
OpenSwathWorkflow + Calibration:RTNormalization:InitialQualityCutoff double 0.5
OpenSwathWorkflow + Calibration:RTNormalization:lowess:auto_span_grid string 0.005,0.01,0.05,0.15,0.25,0.30,0.50,0.70,0.90
OpenSwathWorkflow + Calibration:RTNormalization:lowess:auto_span_max double 0.8 :0.99
OpenSwathWorkflow + Calibration:RTNormalization:lowess:auto_span_min double 0.15 1.0e-03:
OpenSwathWorkflow + Calibration:RTNormalization:lowess:auto_span string true true,false
OpenSwathWorkflow + Calibration:RTNormalization:lowess:span double 0.05 0.0:1.0
OpenSwathWorkflow + Calibration:RTNormalization:MinBinsFilled int 8
OpenSwathWorkflow + Calibration:RTNormalization:MinPeptidesPerBin int 1
OpenSwathWorkflow + Calibration:RTNormalization:NrRTBins int 10
OpenSwathWorkflow + Calibration:RTNormalization:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathWorkflow + Calibration:RTNormalization:OverallQualityCutoff double 5.5
OpenSwathWorkflow + Calibration:RTNormalization:RANSACMaxIterations int 1000
OpenSwathWorkflow + Calibration:RTNormalization:RANSACMaxPercentRTThreshold int 3
OpenSwathWorkflow + Calibration:RTNormalization:RANSACSamplingSize int 10
OpenSwathWorkflow + Calibration:RTNormalization:useIterativeChauvenet bool false
OpenSwathWorkflow + Calibration:rt_norm string
OpenSwathWorkflow + Calibration:tr_irt_nonlinear string
OpenSwathWorkflow + Calibration:tr_irt_priority_sampling string
OpenSwathWorkflow + Calibration:tr_irt string
OpenSwathWorkflow + estimate_extraction_windows string all
OpenSwathWorkflow + im_estimation_padding_factor double 1.0 1.0:
OpenSwathWorkflow + irt_nonlinear_rt_extraction_window double 600.0 -1.0:
OpenSwathWorkflow + mz_estimation_padding_factor double 1.0 1.0:
OpenSwathWorkflow + rt_estimation_padding_factor double 1.3 1.0:
OpenSwathWorkflow - RTNormalization:alignmentMethod string linear linear,interpolated,lowess,b_spline
OpenSwathWorkflow - RTNormalization:b_spline:num_nodes int 5 0:
OpenSwathWorkflow - RTNormalization:estimateBestPeptides bool false
OpenSwathWorkflow - RTNormalization:InitialQualityCutoff double 0.5
OpenSwathWorkflow - RTNormalization:lowess:span double 0.05 0.0:1.0
OpenSwathWorkflow - RTNormalization:MinBinsFilled int 8
OpenSwathWorkflow - RTNormalization:MinPeptidesPerBin int 1
OpenSwathWorkflow - RTNormalization:NrRTBins int 10
OpenSwathWorkflow - RTNormalization:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathWorkflow - RTNormalization:OverallQualityCutoff double 5.5
OpenSwathWorkflow - RTNormalization:RANSACMaxIterations int 1000
OpenSwathWorkflow - RTNormalization:RANSACMaxPercentRTThreshold int 3
OpenSwathWorkflow - RTNormalization:RANSACSamplingSize int 10
OpenSwathWorkflow - RTNormalization:useIterativeChauvenet bool false
OpenSwathWorkflow - rt_norm input-file *.trafoXML
OpenSwathWorkflow - tr_irt input-file *.traML,*.tsv,*.pqp
OpenSwathWorkflow - tr_irt_nonlinear input-file *.traML,*.tsv,*.pqp
PeptideIndexer - enzyme:name string auto auto,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Trypsin,Arg-C,Chymotrypsin/P,CNBr,Formic_acid,Lys-C/P,PepsinA,TrypChymo,Trypsin/P
PeptideIndexer + enzyme:name string auto auto,no cleavage,unspecific cleavage,Trypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
ProteinQuantifier + file_and_channel_level_output bool false
ProteomicsLFQ + Alignment:model:lowess:auto_k_folds int 5 2:
ProteomicsLFQ + Alignment:model:lowess:auto_metric string mae p90,p95,p99,rmse,mae
ProteomicsLFQ + Alignment:model:lowess:auto_min_neighbors int 5 3:
ProteomicsLFQ + Alignment:model:lowess:auto_span bool false
ProteomicsLFQ + Alignment:model:lowess:auto_span_grid string
ProteomicsLFQ + Alignment:model:lowess:auto_span_max double 0.8 :0.99
ProteomicsLFQ + Alignment:model:lowess:auto_span_min double 0.15 1.0e-03:
ProteomicsLFQ + PeptideQuantification:extract:IM_window double 0.06 0.0:
ProteomicsLFQ + PeptideQuantification:faims:merge_features string true true,false
RNADigestor - enzyme string RNase_T1 RNase_4c,mazF,colicin_E5,no cleavage,unspecific cleavage,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,RNase_4,RNase_4p,RNase_T1_Phosphatase,RNase_T1
RNADigestor + enzyme string RNase_T1 RNase_T1_Phosphatase,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,RNase_4,RNase_T1,RNase_4p,RNase_4c,mazF,colicin_E5,no cleavage,unspecific cleavage
SageAdapter + enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,leukocyte elastase,proline endopeptidase,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
SageAdapter - enzyme string Trypsin Lys-C,Lys-N,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,proline-endopeptidase/HKR,Glu-C+P,Trypsin,Arg-C,unspecific cleavage,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage
SageAdapter - PeptideIndexing:enzyme:name string auto auto,Arg-C/P,Asp-N,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Trypsin,Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Arg-C,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
SageAdapter + PeptideIndexing:enzyme:name string auto auto,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin,Arg-C,Arg-C/P,unspecific cleavage,Lys-C/P,PepsinA,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
SimpleSearchEngine - Search:enzyme string Trypsin Chymotrypsin/P,CNBr,Formic_acid,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
SimpleSearchEngine + Search:enzyme string Trypsin Lys-C,Lys-N,V8-E,leukocyte elastase,proline endopeptidase,no cleavage,unspecific cleavage,Trypsin,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,TrypChymo,Trypsin/P,V8-DE,Lys-C/P,PepsinA,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic
TextExporter + id:annotations string none none,default