On this pageDear OpenMS-Users,
we are proud to announce the release of OpenMS 3.0.0. Grab it here
In the following you find all important changes to the previous version:
- full release
- OpenSwath: Add support for diaPASEF data with overlapping m/z and IM windows, and add new outputs on ion mobility features (delta_im)
- OpenSwath: Fix duplicated transition error when multiple genes map to a single peptide (#5653)
- TOPPView: TheoreticalSpectrumGenerationDialog now supports generation of isotope patterns for metabolites
- pyopenms: pyopenms-extra is renamed to pyopenms-docs.
- Add extractSpectra to TargetedSpectraExtractor with support of MS1 features
- TargetedSpectraExtractor::searchSpectrum added an option to add unknown features to the result featureMap
- Fixed race condition when logging messages.
- Added the support for ‘no cleavage’ for XTandemAdapter and CometAdapter (#6133).
- ParamEditor with more convenient StringList editing (#5135)
- TOPPAS: add a
recent filessubmenu - removed InspectAdapter
- removed OMSSAAdapter
- removed MyriMatchAdapter
- removed Crux
- OpenMS documentation is moved to openms.readthedocs.io/en/latest. OpenMS API reference and advanced developer documentation remains inside OpenMS doxygen documentation.
- Add support for user defined ribonucleotides with phosphorothioate linkages
- Add support for JSON based ribonucleotides and updated to latest Modomics database
- fix bug in GaussFilter when using ppm as width (#6830)
- Add support to load parameter values from a JSON formatted .json file. (Accessible via -ini. This will be helpful for Common Workflow Language users and others)
New Tools:
- FLASHDeconv – Ultra-fast high-quality deconvolution enables online processing of top-down MS data (TOPP)
- FLASHDeconvWizard – An GUI assistant for FLASHDeconv execution.
Additionally, the following changes were made to parameters of our TOPP tools:
| Tool name | Added/removed | Parameter name | Type | Default value | Restrictions | Supported formats |
|---|---|---|---|---|---|---|
| AssayGeneratorMetabo | + | fingerid:db | string | |||
| AssayGeneratorMetabo | + | project:loglevel | string | |||
| AssayGeneratorMetabo | + | project:maxmz | int | -1 | ||
| AssayGeneratorMetabo | + | read_sirius_stdout | bool | false | ||
| AssayGeneratorMetabo | + | sirius:candidates | int | 10 | 0: | |
| AssayGeneratorMetabo | + | sirius:candidates_per_ion | int | 1 | ||
| AssayGeneratorMetabo | + | sirius:db | string | none | ||
| AssayGeneratorMetabo | + | sirius:elements_considered | string | SBrClBSe | ||
| AssayGeneratorMetabo | + | sirius:elements_enforced | string | CHNOP | ||
| AssayGeneratorMetabo | + | sirius:formulas | string | |||
| AssayGeneratorMetabo | + | sirius:ions_considered | string | [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]- | ||
| AssayGeneratorMetabo | + | sirius:profile | string | default | default,qtof,orbitrap,fticr | |
| AssayGeneratorMetabo | + | sirius:solver | string | CLP | ||
| AssayGeneratorMetabo | + | sirius:tree_timeout | int | 100 | 0: | |
| AssayGeneratorMetabo | - | fingerid:candidates | int | 10 | 1: | |
| AssayGeneratorMetabo | - | fingerid:db | string | BIO | ||
| AssayGeneratorMetabo | - | sirius:candidates | int | 5 | 1: | |
| AssayGeneratorMetabo | - | sirius:candidates_per_ion | int | -1 | ||
| 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:profile | string | qtof | default,qtof,orbitrap,fticr | |
| AssayGeneratorMetabo | - | sirius:tree_timeout | int | 0 | 0: | |
| CometAdapter | + | PeptideIndexing:allow_nterm_protein_cleavage | string | true | true,false | |
| CometAdapter | + | PeptideIndexing:enzyme:name | string | auto | auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| CometAdapter | + | enzyme | string | Trypsin | Trypsin,Arg-C,Chymotrypsin,CNBr,Asp-N,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage | |
| CometAdapter | + | second_enzyme | string | Trypsin,Arg-C,Chymotrypsin,CNBr,Asp-N,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage | ||
| CometAdapter | - | PeptideIndexing:enzyme:name | string | auto | auto,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| CometAdapter | - | enzyme | string | Trypsin | Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage | |
| CometAdapter | - | second_enzyme | string | Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage | ||
| CompNovo | + | algorithm:tryptic_only | string | true | true,false | |
| CompNovo | - | algorithm:tryptic_only | string | true | ||
| CompNovoCID | + | algorithm:tryptic_only | string | true | true,false | |
| CompNovoCID | - | algorithm:tryptic_only | string | true | ||
| DecoyDatabase | + | enzyme | string | Trypsin | Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| DecoyDatabase | - | enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| Digestor | + | enzyme | string | Trypsin | Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| Digestor | - | enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| DigestorMotif | + | enzyme | string | Trypsin | Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,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,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,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,no cleavage,unspecific cleavage | |
| FalseDiscoveryRate | + | peptide | bool | false | ||
| FeatureFinderIdentification | + | min_psm_cutoff | string | none | ||
| FeatureFinderIdentification | + | svm:log2_p | double | |||
| FeatureFinderMetaboIdent | + | candidates_out | output-file | |||
| FeatureFinderMetaboIdent | - | candidates_out | output-file | *.featureXML | ||
| FidoAdapter | + | accuracy | string | best | best,relaxed,sloppy | |
| FidoAdapter | - | accuracy | string | ,best,relaxed,sloppy | ||
| FileConverter | + | include_noise | bool | false | ||
| FileConverter | + | no_zlib_compression | bool | false | ||
| FileFilter | + | f_and_c:remove_hull | bool | false | ||
| GNPSExport | + | out_meta_values | output-file | *.tsv | ||
| GNPSExport | + | out_pairs | output-file | *.csv | ||
| GNPSExport | + | out_quantification | output-file | *.txt | ||
| IDFileConverter | + | fasta_to_mzml:enzyme | string | Trypsin | Chymotrypsin,Trypsin,Arg-C,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| IDFileConverter | - | fasta_to_mzml:enzyme | string | Trypsin | Asp-N,Asp-N/B,Asp-N_ambic,Trypsin,Arg-C,Arg-C/P,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,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 | |
| IDFilter | + | in_silico_digestion:enzyme | string | Trypsin | Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| IDFilter | + | missed_cleavages:enzyme | string | Trypsin | Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| IDFilter | - | in_silico_digestion:enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| IDFilter | - | missed_cleavages:enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| IDRipper | + | out | output-prefix | |||
| IDRipper | - | out | output-file | |||
| IsobaricAnalyzer | + | extraction:select_activation | string | auto | auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,any | |
| IsobaricAnalyzer | + | tmt18plex:channel_126_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_127C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_127N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_128C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_128N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_129C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_129N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_130C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_130N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_131C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_131N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_132C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_132N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_133C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_133N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_134C_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_134N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:channel_135N_description | string | |||
| IsobaricAnalyzer | + | tmt18plex:correction_matrix | string | |||
| IsobaricAnalyzer | + | tmt18plex:reference_channel | string | 126 | 126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C,132N,132C,133N,133C,134N,134C,135N | |
| IsobaricAnalyzer | + | type | string | itraq4plex | itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt18plex,tmt6plex | |
| IsobaricAnalyzer | - | extraction:select_activation | string | auto | auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation, | |
| IsobaricAnalyzer | - | type | string | itraq4plex | itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt6plex | |
| MSFraggerAdapter | + | PeptideIndexing:allow_nterm_protein_cleavage | string | true | true,false | |
| MSFraggerAdapter | + | PeptideIndexing:enzyme:name | string | auto | auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,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 | unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage | |
| MSFraggerAdapter | - | PeptideIndexing:enzyme:name | string | auto | auto,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,no cleavage,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin,Arg-C,Arg-C/P,unspecific cleavage | |
| MSFraggerAdapter | - | digest:search_enzyme_name | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| MSGFPlusAdapter | + | PeptideIndexing:allow_nterm_protein_cleavage | string | true | true,false | |
| MSGFPlusAdapter | + | PeptideIndexing:enzyme:name | string | auto | auto,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| MSGFPlusAdapter | - | PeptideIndexing:enzyme:name | string | auto | auto,Trypsin,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,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| MSGFPlusAdapter | - | add_decoys | bool | false | ||
| MSSimulator | + | algorithm:MSSim:Digestion:enzyme | string | Trypsin | unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage | |
| MSSimulator | - | algorithm:MSSim:Digestion:enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| MapAlignerIdentification | + | model:linear:x_weight | string | x | 1/x,1/x2,ln(x),x | |
| MapAlignerIdentification | + | model:linear:y_weight | string | y | 1/y,1/y2,ln(y),y | |
| MapAlignerIdentification | - | model:linear:x_weight | string | 1/x,1/x2,ln(x), | ||
| MapAlignerIdentification | - | model:linear:y_weight | string | 1/y,1/y2,ln(y), | ||
| MapAlignerSpectrum | + | model:linear:x_weight | string | x | 1/x,1/x2,ln(x),x | |
| MapAlignerSpectrum | + | model:linear:y_weight | string | y | 1/y,1/y2,ln(y),y | |
| MapAlignerSpectrum | - | model:linear:x_weight | string | 1/x,1/x2,ln(x), | ||
| MapAlignerSpectrum | - | model:linear:y_weight | string | 1/y,1/y2,ln(y), | ||
| MapAlignerTreeGuided | + | algorithm:model:linear:x_weight | string | x | 1/x,1/x2,ln(x),x | |
| MapAlignerTreeGuided | + | algorithm:model:linear:y_weight | string | y | 1/y,1/y2,ln(y),y | |
| MapAlignerTreeGuided | - | algorithm:model:linear:x_weight | string | 1/x,1/x2,ln(x), | ||
| MapAlignerTreeGuided | - | algorithm:model:linear:y_weight | string | 1/y,1/y2,ln(y), | ||
| MapRTTransformer | + | model:linear:x_weight | string | x | 1/x,1/x2,ln(x),x | |
| MapRTTransformer | + | model:linear:y_weight | string | y | 1/y,1/y2,ln(y),y | |
| MapRTTransformer | - | model:linear:x_weight | string | 1/x,1/x2,ln(x), | ||
| MapRTTransformer | - | model:linear:y_weight | string | 1/y,1/y2,ln(y), | ||
| MetaboliteAdductDecharger | + | algorithm:MetaboliteFeatureDeconvolution:negative_mode | bool | false | ||
| MetaboliteAdductDecharger | + | algorithm:MetaboliteFeatureDeconvolution:use_minority_bound | string | true | true,false | |
| MetaboliteAdductDecharger | - | algorithm:MetaboliteFeatureDeconvolution:negative_mode | string | false | ||
| MetaboliteAdductDecharger | - | algorithm:MetaboliteFeatureDeconvolution:use_minority_bound | string | true | ||
| MetaboliteSpectralMatcher | + | algorithm:merge_spectra | string | true | true,false | |
| MetaboliteSpectralMatcher | + | database | input-file | .mzML,.msp,*.mgf | ||
| MetaboliteSpectralMatcher | + | out_spectra | output-file | *.mzML | ||
| MetaboliteSpectralMatcher | - | database | input-file | *.mzML | ||
| MzMLSplitter | + | out | output-prefix | |||
| MzMLSplitter | - | out | string | |||
| NoiseFilterGaussian | + | algorithm:write_log_messages | bool | false | ||
| NoiseFilterGaussian | - | algorithm:write_log_messages | string | false | ||
| NucleicAcidSearchEngine | + | modifications:variable | 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 | - | modifications:variable | string | m1Am,m1Gm,m1Im,m1acp3Y,m1A,m1G,m1I,m1Y,m28A,msms2i6A,ges2U,k2C,m2A,ms2ct6A,ms2io6A,ms2hn6A,ms2i6A,ms2m6A,ms2t6A,se2U,s2Um,s2C,s2U,Am,Cm,Gm,Im,Ym,Um,mcmo5Um,Ar(p),Gr(p),(pN)2'3'>p,hm5Cm,m3Um,acp3D,acp3Y,acp3U,m3C,m3Y,m3U,imG-14,s4U,m5Cm,m5Um,mchm5Um,mchm5U,inm5s2U,inm5Um,inm5U,nm5ges2U,nm5se2U,nm5s2U,nm5U,nchm5U,ncm5s2U,ncm5Um,ncm5U,chm5U,cm5s2U,cmnm5ges2U,cmnm5se2U,cmnm5s2U,cmnm5Um,cmnm5U,cm5U,cnm5U,f5Cm,f5C,ho5C,hm5C,ho5U,mcm5s2U,mcm5Um,mcm5U,mo5U,m5s2U,mnm5ges2U,mnm5se2U,mnm5s2U,mnm5U,m5C,m5D,m5U,tm5s2U,tm5U,CoA(pN),acCoA(pN),malonyl-CoA(pN),succinyl-CoA(pN),p(pN),5'-OH-N,(pN),NAD(pN),pp(pN),yW-86,yW-72,yW-58,preQ1tRNA,preQ0tRNA,m7G,m7Gpp(pN),m8A,m2Gm,m27Gm,m27G,m27Gpp(pN),m22Gm,m227G,m227Gpp(pN),m22G,m2G,m4Cm,m44Cm,m44C,ac4Cm,ac4C,m4C,m6Am,m66Am,m66A,io6A,ac6A,f6A,g6A,hm6A,hn6A,i6A,m6t6A,m6A,t6A,Qbase,C+,mm(pN),m(pN),G+,ct6A,D,oQ,galQ,mpp(pN),gluQ,pG(pN),Gpp(pN),ht6A,OHyW,I,imG2,manQ,OHyWy,mimG,o2yW,preQ0base,preQ1base,Y,Q,OHyWx,Xm,xX,xA,xC,xG,xU,N,cmo5U,mcmo5U,yW,imG,dA,dC,dG,dU,dT,3'-p,5'-p,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? | ||
| OpenPepXL | + | peptide:enzyme | string | Trypsin | Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| OpenPepXL | - | peptide:enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| OpenPepXLLF | + | peptide:enzyme | string | Trypsin | Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| OpenPepXLLF | - | peptide:enzyme | string | Trypsin | Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| OpenSwathAnalyzer | + | algorithm:strict | string | true | true,false | |
| OpenSwathAnalyzer | - | algorithm:strict | string | true | ||
| OpenSwathFileSplitter | + | outputDirectory | output-prefix | ./ | ||
| OpenSwathFileSplitter | - | outputDirectory | string | ./ | ||
| OpenSwathRTNormalizer | + | algorithm:strict | string | true | true,false | |
| OpenSwathRTNormalizer | - | algorithm:strict | string | true | ||
| OpenSwathWorkflow | + | Scoring:strict | string | true | true,false | |
| OpenSwathWorkflow | + | pasef | bool | false | ||
| OpenSwathWorkflow | - | Scoring:strict | string | true | ||
| PeptideIndexer | + | allow_nterm_protein_cleavage | string | true | true,false | |
| PeptideIndexer | + | enzyme:name | string | auto | auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| PeptideIndexer | - | enzyme:name | string | auto | auto,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| PrecursorIonSelector | + | algorithm:Preprocessing:store_peptide_sequences | bool | false | ||
| PrecursorIonSelector | - | algorithm:Preprocessing:store_peptide_sequences | string | false | ||
| ProteinQuantifier | + | method | string | top | top,iBAQ | |
| ProteinQuantifier | + | top:N | int | 3 | 0: | |
| ProteinQuantifier | + | top:aggregate | string | median | median,mean,weighted_mean,sum | |
| ProteinQuantifier | + | top:include_all | bool | false | ||
| ProteinQuantifier | - | average | string | median | median,mean,weighted_mean,sum | |
| ProteinQuantifier | - | include_all | bool | false | ||
| ProteinQuantifier | - | top | int | 3 | 0: | |
| ProteomicsLFQ | + | Alignment:model:linear:x_weight | string | x | 1/x,1/x2,ln(x),x | |
| ProteomicsLFQ | + | Alignment:model:linear:y_weight | string | y | 1/y,1/y2,ln(y),y | |
| ProteomicsLFQ | + | FDR_type | string | PSM | PSM,PSM+peptide | |
| ProteomicsLFQ | + | PeptideQuantification:min_psm_cutoff | string | none | ||
| ProteomicsLFQ | + | PeptideQuantification:svm:log2_p | double | |||
| ProteomicsLFQ | + | ProteinQuantification:method | string | top | top,iBAQ | |
| ProteomicsLFQ | + | ProteinQuantification:top:N | int | 3 | 0: | |
| ProteomicsLFQ | + | ProteinQuantification:top:aggregate | string | median | median,mean,weighted_mean,sum | |
| ProteomicsLFQ | + | ProteinQuantification:top:include_all | string | true | true,false | |
| ProteomicsLFQ | + | picked_proteinFDR | bool | false | ||
| ProteomicsLFQ | - | Alignment:model:linear:x_weight | string | 1/x,1/x2,ln(x), | ||
| ProteomicsLFQ | - | Alignment:model:linear:y_weight | string | 1/y,1/y2,ln(y), | ||
| ProteomicsLFQ | - | ProteinQuantification:average | string | median | median,mean,weighted_mean,sum | |
| ProteomicsLFQ | - | ProteinQuantification:include_all | string | true | true,false | |
| ProteomicsLFQ | - | ProteinQuantification:top | int | 3 | 0: | |
| ProteomicsLFQ | - | picked_proteinFDR | string | false | ||
| QualityControl | + | in_fasta | input-file | *.fasta | ||
| QualityControl | + | out_msms | string | |||
| RNPxlSearch | + | peptide:enzyme | string | Trypsin | Arg-C,Trypsin,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| RNPxlSearch | - | peptide:enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| SimpleSearchEngine | + | Search:enzyme | string | Trypsin | Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| SimpleSearchEngine | - | Search:enzyme | string | Trypsin | Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,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,no cleavage,unspecific cleavage | |
| SiriusAdapter | + | fingerid:db | string | |||
| SiriusAdapter | + | out_annotated_spectra | output-file | *.mzML | ||
| SiriusAdapter | + | project:loglevel | string | |||
| SiriusAdapter | + | project:maxmz | int | -1 | ||
| SiriusAdapter | + | read_sirius_stdout | bool | false | ||
| SiriusAdapter | + | sirius:candidates | int | 10 | 0: | |
| SiriusAdapter | + | sirius:candidates_per_ion | int | 1 | ||
| SiriusAdapter | + | sirius:db | string | none | ||
| SiriusAdapter | + | sirius:elements_considered | string | SBrClBSe | ||
| SiriusAdapter | + | sirius:elements_enforced | string | CHNOP | ||
| SiriusAdapter | + | sirius:formulas | string | |||
| SiriusAdapter | + | sirius:ions_considered | string | [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]- | ||
| SiriusAdapter | + | sirius:profile | string | default | default,qtof,orbitrap,fticr | |
| SiriusAdapter | + | sirius:solver | string | CLP | ||
| SiriusAdapter | + | sirius:tree_timeout | int | 100 | 0: | |
| SiriusAdapter | + | sirius_user_email | string | |||
| SiriusAdapter | + | sirius_user_password | string | |||
| SiriusAdapter | - | fingerid:candidates | int | 10 | 1: | |
| SiriusAdapter | - | fingerid:db | string | BIO | ||
| SiriusAdapter | - | project:processors | int | 1 | ||
| SiriusAdapter | - | sirius:candidates | int | 5 | 1: | |
| SiriusAdapter | - | sirius:candidates_per_ion | int | -1 | ||
| 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:profile | string | qtof | default,qtof,orbitrap,fticr | |
| SiriusAdapter | - | sirius:tree_timeout | int | 0 | 0: | |
| SpectraMerger | + | algorithm:average_gaussian:ms_level | int | 1 | 0: | |
| SpectraMerger | + | algorithm:average_gaussian:precursor_mass_tol | double | 0.0 | 0.0: | |
| SpectraMerger | + | algorithm:average_gaussian:precursor_max_charge | int | 1 | 1: | |
| SpectraMerger | + | algorithm:average_tophat:ms_level | int | 1 | 0: | |
| SpectraMerger | + | algorithm:precursor_method:mass_tolerance | double | 0.0 | 0.0: | |
| SpectraMerger | - | algorithm:average_gaussian:ms_level | int | 1 | 1: | |
| SpectraMerger | - | algorithm:average_tophat:ms_level | int | 1 | 1: | |
| TextExporter | + | consensus:add_metavalues | bool | false | ||
| XTandemAdapter | + | PeptideIndexing:allow_nterm_protein_cleavage | string | true | true,false | |
| XTandemAdapter | + | PeptideIndexing:enzyme:name | string | auto | auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,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,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | |
| XTandemAdapter | + | enzyme | string | Trypsin | Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,no cleavage,unspecific cleavage | |
| XTandemAdapter | - | PeptideIndexing:enzyme:name | string | auto | auto,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,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Trypsin | |
| XTandemAdapter | - | enzyme | string | Trypsin | Asp-N,Asp-N/B,Asp-N_ambic,unspecific cleavage,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,Arg-C |
Best regards, The OpenMS-Developers