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CHANGELOG
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CHANGELOG
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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS Proteomics Pipeline", collection of chainable tools for flexible HPLC/MS workflows
TOPPAS - "The OpenMS Proteomics Pipeline Assistant", graphical tool to interactively build and run HPLC/MS workflows
TOPPView - Versatile viewer for HPLC/MS data
INI file - parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor - graphical parameter editor for INI files
Parameters - list of algorithm or TOPP tool parameters that changed in this release
------------------------------------------------------------------------------------------
---- OpenMS 2.4 ----
------------------------------------------------------------------------------------------
OpenMS 2.4 introduces changes from 322 pull requests including new features and bug fixes.
Notable changes since version 2.3 are:
Dependencies:
- Switch to Qt 5 (>= 5.5)
Documentation:
- New developer documentation to get started developing tools with OpenMS
Library:
- Improved mass calculations for isotope distributions
- Moved tool code from the tool to the library
- BinnedSpectrum now also supports offsets
- Improved peak type estimation
- Improved adduct grouping
- New EMG fitter for peak intensity imputation
- Targeted / untargeted spectra extraction and matching
- Spectra matching against a spectra library, using contrast angle similary function
- More precise peak integration (trapezoid, simpson)
New tools:
- AssayGeneratorMetabo -- Assay library generation from DDA data (Metabolomics) (UTIL)
- ClusterMassTraces -- Creates pseudo spectra (UTIL)
- ClusterMassTracesByPrecursor -- Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile (UTIL)
- CruxAdapter -- Identifies MS/MS spectra using Crux (TOPP)
- MSFraggerAdapter -- Peptide Identification with MSFragger (UTIL)
- MSstatsConverter -- Converter to input for MSstats (UTIL)
- MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate (TOPP)
- NovorAdapter -- Template for Tool creation (UTIL)
- RNADigestor -- Digests an RNA sequence database in-silico (UTIL)
Deprecated and removed tools:
- AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples (TOPP)
- IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value (UTIL)
- IDEvaluatorGUI -- Computes a 'q-value vs. #PSM' plot to visualize the number identifications for a certain q-value (UTIL)
- RNPxl -- Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)
Changed Tools:
- SiriusAdapter now supports several input data
- FileFilter now supports filtering spectra by similarity
- PeptideIndexer now supports automatic detection of decoy suffix/prefix string and position
- PeakPickerHiRes now supports automatic detection and picking of profile spectra
- Support for MSFragger search engine through MSFraggerAdapter
- Support for Crux search engine through CruxAdapter
- Support for Maracluster through MaraClusterAdapter
- OpenPepXL was improved in efficiency and usability
- IDFileConverter now supports the Cross-Linking MS specific xquest.xml format
TOPPView:
- Improved visualization of identification results and ion annotations
- Support for visualization of Ion Mobility and DIA data
Major changes in functionality:
- None
File formats:
- Importer for MSP files
Scripts:
- None
Databases:
- None
Third-party software:
- New: maracluster (0.05)
- Update: MS-GF+ to Release (2018.01.30)
- Update: Sirius 4 for Windows 64bit, Linux 64bit, and MacOS 64bit
- Update: Crux (crux-3.1.8b78546) on all 64bit platforms.
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + out output-file *.mzTab
AccurateMassSearch - out output-file *.tsv
CometAdapter + allowed_missed_cleavages int 0 0:5
CometAdapter + enzyme string Trypsin glutamyl endopeptidase,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,unspecific cleavage,Trypsin
CometAdapter + fragment_bin_offset double 0 0:1
CometAdapter + fragment_bin_tolerance double 0.02 0.01:
CometAdapter + isotope_error string off off,0/1,0/1/2,-1/0/1/2/3,-8/-4/0/4/8
CometAdapter + mass_offsets double
CometAdapter + max_fragment_charge int 3 1:5
CometAdapter + max_precursor_charge int 5 1:9
CometAdapter + minimum_intensity double 0 0:
CometAdapter + override_charge string keep known search unknown keep any known,ignore known,ignore outside range,keep known search unknown
CometAdapter + remove_precursor_peak string no no,yes,charge_reduced,phosphate_loss
CometAdapter + remove_precursor_tolerance double 1.5
CometAdapter + require_variable_mod string false true,false
CometAdapter + spectrum_batch_size int 20000 0:
CometAdapter - allowed_missed_cleavages int 1
CometAdapter - enzyme string Trypsin unspecific cleavage,Lys-N,Lys-C,Chymotrypsin,CNBr,glutamyl endopeptidase,PepsinA,Arg-C,Trypsin/P,Trypsin,Asp-N
CometAdapter - fragment_bin_offset double 0.25
CometAdapter - fragment_bin_tolerance double 1.0005
CometAdapter - isotope_error string off off,-1/0/1/2/3,-8/-4/0/4/8
CometAdapter - mass_offsets double 0
CometAdapter - max_fragment_charge int 3
CometAdapter - max_precursor_charge string 0+
CometAdapter - minimum_intensity int 0
CometAdapter - override_charge string keep any known keep any known,ignore known,ignore outside range,keep known search unknown
CometAdapter - remove_precursor_peak string no no,yes,all
CometAdapter - remove_precursor_tolerance int 1
CometAdapter - spectrum_batch_size int 1000
DecoyDatabase + Decoy:keepPeptideCTerm string true true,false
DecoyDatabase + Decoy:keepPeptideNTerm string true true,false
DecoyDatabase + Decoy:non_shuffle_pattern string
DecoyDatabase + enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P
DecoyDatabase + seed string 1
DecoyDatabase + shuffle_max_attempts int 30
DecoyDatabase + shuffle_sequence_identity_threshold double 0.5
Digestor + FASTA:ID string parent parent,number,both
Digestor + FASTA:description string remove remove,keep
Digestor + enzyme string Trypsin Asp-N,Trypsin,Arg-C/P,Chymotrypsin/P,CNBr,Arg-C,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin
Digestor - enzyme string Trypsin glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-N_ambic,V8-DE,CNBr,leukocyte elastase,proline endopeptidase,Lys-N,Lys-C/P,Arg-C/P,Chymotrypsin,Formic_acid,Chymotrypsin/P,V8-E,Alpha-lytic protease,PepsinA,TrypChymo,Trypsin/P
DigestorMotif + enzyme string Trypsin Trypsin,Arg-C/P,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,Asp-N,Arg-C,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-N_ambic,unspecific cleavage,Chymotrypsin,Asp-N/B,Chymotrypsin/P
DigestorMotif - enzyme string Trypsin Asp-N_ambic,Trypsin,Asp-N/B,Chymotrypsin/P,Chymotrypsin,Trypsin/P,V8-DE,V8-E,PepsinA,TrypChymo,glutamyl endopeptidase,Lys-C/P,Formic_acid,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Lys-C,Lys-N,Arg-C,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,CNBr
FalseDiscoveryRate + algorithm:add_decoy_proteins string false true,false
FeatureFinderIdentification + debug int 0 0:
FeatureFinderIdentification - debug int 0
FeatureFinderMetabo + algorithm:ffm:remove_single_traces string false false,true
FeatureFinderMultiplex + algorithm:averagine_similarity_scaling double 0.95 0:1
FeatureFinderMultiplex + algorithm:rt_band double 0 0:
FeatureFinderMultiplex + out output-file *.featureXML
FeatureFinderMultiplex + out_multiplets output-file *.consensusXML
FeatureFinderMultiplex - algorithm:averagine_similarity_scaling double 0.75 0:1
FeatureFinderMultiplex - out output-file *.consensusXML
FeatureFinderMultiplex - out_features output-file *.featureXML
FeatureFinderMultiplex - out_mzq output-file *.mzq
FeatureLinkerUnlabeled + algorithm:ignore_adduct string true true,false
FeatureLinkerUnlabeledKD + algorithm:ignore_adduct string true true,false
FeatureLinkerUnlabeledQT + algorithm:ignore_adduct string true true,false
FileConverter + convert_to_chromatograms string false true,false
FileFilter + id:sequence_comparison_method string substring substring,exact
FileFilter + peak_options:indexed_file string true true,false
FileFilter + peak_options:numpress:float_da string none none,linear,pic,slof
FileFilter + peak_options:numpress:lossy_mass_accuracy double -1
FileFilter + spectra:blackorwhitelist:blacklist string true false,true
FileFilter + spectra:blackorwhitelist:file input-file *.mzML
FileFilter + spectra:blackorwhitelist:mz double 0.01
FileFilter + spectra:blackorwhitelist:rt double 0.01
FileFilter + spectra:blackorwhitelist:similarity_threshold double -1 -1:1
FileFilter + spectra:blackorwhitelist:use_ppm_tolerance string false
FileFilter - peak_options:indexed_file string false true,false
FileFilter - peak_options:numpress:intensity_error double 0.0001
FileFilter - peak_options:numpress:masstime_error double 0.0001
IDConflictResolver + resolve_between_features string off off,highest_intensity
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
IDFileConverter - in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid
IDFileConverter - out output-file *.idXML,*.mzid,*.pepXML,*.FASTA
IDFileConverter - out_type string idXML,mzid,pepXML,FASTA
IDFilter + in_silico_digestion:enzyme string Trypsin Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Arg-C/P,no cleavage,unspecific cleavage
IDFilter + in_silico_digestion:fasta input-file *.fasta
IDFilter + in_silico_digestion:methionine_cleavage string false true,false
IDFilter + in_silico_digestion:missed_cleavages int -1 -1:
IDFilter + in_silico_digestion:specificity string full full,semi,none
IDFilter + missed_cleavages:enzyme string Trypsin Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Arg-C/P,no cleavage,unspecific cleavage
IDFilter + missed_cleavages:number_of_missed_cleavages string :
IDFilter - digest:enzyme string Trypsin Lys-C,V8-E,Trypsin/P,no cleavage,V8-DE,CNBr,Lys-C/P,Formic_acid,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,Asp-N/B,Arg-C/P,proline endopeptidase,TrypChymo,Arg-C,leukocyte elastase,Chymotrypsin/P,Asp-N,Chymotrypsin,Trypsin,PepsinA,Asp-N_ambic,glutamyl endopeptidase,Lys-N
IDFilter - digest:fasta input-file *.fasta
IDFilter - digest:methionine_cleavage string false true,false
IDFilter - digest:missed_cleavages int -1 -1:
IDFilter - digest:specificity string full full,semi,none
IsobaricAnalyzer - id_pool string
MRMMapper + algorithm:error_on_unmapped string false true,false
MRMMapper + algorithm:map_multiple_assays string false true,false
MRMMapper + algorithm:precursor_tolerance double 0.1
MRMMapper + algorithm:product_tolerance double 0.1
MRMMapper - allow_multiple_mappings string false true,false
MRMMapper - no-strict string false true,false
MRMMapper - precursor_tolerance double 0.1
MRMMapper - product_tolerance double 0.1
MRMTransitionGroupPicker + algorithm:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max
MRMTransitionGroupPicker + algorithm:PeakIntegrator:fit_EMG string false false,true
MRMTransitionGroupPicker + algorithm:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid
MRMTransitionGroupPicker + algorithm:background_subtraction string none none,original,exact
MRMTransitionGroupPicker + algorithm:boundary_selection_method string largest largest,widest
MRMTransitionGroupPicker + algorithm:compute_peak_shape_metrics string false true,false
MRMTransitionGroupPicker + algorithm:compute_total_mi string false true,false
MRMTransitionGroupPicker + algorithm:peak_integration string original original,smoothed
MRMTransitionGroupPicker + algorithm:use_consensus string true true,false
MRMTransitionGroupPicker - algorithm:background_subtraction string none none,smoothed,original
MSGFPlusAdapter + add_features string true true,false
MSGFPlusAdapter + protocol string automatic automatic,phospho,iTRAQ,iTRAQ_phospho,TMT,none
MSGFPlusAdapter - add_features string false true,false
MSGFPlusAdapter - protocol string none none,phospho,iTRAQ,iTRAQ_phospho,TMT
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin Trypsin,Asp-N/B,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,CNBr,Formic_acid,Lys-C,unspecific cleavage,Chymotrypsin,Asp-N_ambic,Arg-C/P,Chymotrypsin/P,Asp-N,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin PepsinA,2-iodobenzoate,no cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-N_ambic,CNBr,Alpha-lytic protease,glutamyl endopeptidase,Lys-N,Lys-C/P,Chymotrypsin,Formic_acid,Chymotrypsin/P,Arg-C/P,leukocyte elastase,proline endopeptidase,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage
MapAlignerIdentification + model:linear:x_datum_max double 1e+15
MapAlignerIdentification + model:linear:x_datum_min double 1e-15
MapAlignerIdentification + model:linear:x_weight string 1/x,1/x2,ln(x),
MapAlignerIdentification + model:linear:y_datum_max double 1e+15
MapAlignerIdentification + model:linear:y_datum_min double 1e-15
MapAlignerIdentification + model:linear:y_weight string 1/y,1/y2,ln(y),
MapAlignerPoseClustering + algorithm:pairfinder:ignore_adduct string true true,false
MapAlignerPoseClustering + in input-file *.featureXML,*.mzML
MapAlignerPoseClustering + out output-file *.featureXML,*.mzML
MapAlignerPoseClustering + reference:file input-file *.featureXML,*.mzML
MapAlignerPoseClustering - in input-file *.mzML,*.featureXML
MapAlignerPoseClustering - out output-file *.mzML,*.featureXML
MapAlignerPoseClustering - reference:file input-file *.mzML,*.featureXML
MapAlignerSpectrum + model:linear:x_datum_max double 1e+15
MapAlignerSpectrum + model:linear:x_datum_min double 1e-15
MapAlignerSpectrum + model:linear:x_weight string 1/x,1/x2,ln(x),
MapAlignerSpectrum + model:linear:y_datum_max double 1e+15
MapAlignerSpectrum + model:linear:y_datum_min double 1e-15
MapAlignerSpectrum + model:linear:y_weight string 1/y,1/y2,ln(y),
MapRTTransformer + model:linear:x_datum_max double 1e+15
MapRTTransformer + model:linear:x_datum_min double 1e-15
MapRTTransformer + model:linear:x_weight string 1/x,1/x2,ln(x),
MapRTTransformer + model:linear:y_datum_max double 1e+15
MapRTTransformer + model:linear:y_datum_min double 1e-15
MapRTTransformer + model:linear:y_weight string 1/y,1/y2,ln(y),
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:max_minority_bound int 3 0:
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:max_neutrals int 1
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:use_minority_bound string true
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:max_minority_bound int 2 0:
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:max_neutrals int 0
MetaboliteSpectralMatcher + out output-file *.mzTab
MetaboliteSpectralMatcher - out output-file *.tsv
MzTabExporter + out output-file *.mzTab
MzTabExporter - out output-file *.tsv
OMSSAAdapter + enzyme string Trypsin glutamyl endopeptidase,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Arg-C,Asp-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin
OMSSAAdapter - enzyme string Trypsin Trypsin,Arg-C,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,Asp-N,Lys-C,Lys-C/P,Chymotrypsin,CNBr,Formic_acid,unspecific cleavage,Asp-N_ambic
OpenPepXL + algorithm:deisotope string auto true,false,auto
OpenPepXL + ions:a_ions string false true,false
OpenPepXL + ions:b_ions string true true,false
OpenPepXL + ions:c_ions string false true,false
OpenPepXL + ions:neutral_losses string true true,false
OpenPepXL + ions:x_ions string false true,false
OpenPepXL + ions:y_ions string true true,false
OpenPepXL + ions:z_ions string false true,false
OpenPepXL + out_xquest_specxml output-file *.xml,*.spec.xml
OpenPepXL + out_xquestxml output-file *.xml,*.xquest.xml
OpenPepXL + peptide:enzyme string Trypsin 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,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Trypsin,Arg-C,unspecific cleavage
OpenPepXL + precursor:corrections int
OpenPepXL - out_xquest_specxml output-file *.xml
OpenPepXL - out_xquestxml output-file *.xml
OpenPepXL - peptide:enzyme string Trypsin unspecific cleavage,no cleavage,TrypChymo,Lys-C,Lys-N,2-iodobenzoate,V8-E,PepsinA,proline endopeptidase,Trypsin/P,glutamyl endopeptidase,Alpha-lytic protease,V8-DE,Formic_acid,leukocyte elastase,Lys-C/P,Chymotrypsin/P,CNBr,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Arg-C/P,Trypsin,Arg-C
OpenPepXLLF + algorithm:deisotope string auto true,false,auto
OpenPepXLLF + algorithm:number_of_scored_candidates int 10000
OpenPepXLLF + algorithm:pre_scoring string false true,false
OpenPepXLLF + ions:a_ions string false true,false
OpenPepXLLF + ions:b_ions string true true,false
OpenPepXLLF + ions:c_ions string false true,false
OpenPepXLLF + ions:neutral_losses string true true,false
OpenPepXLLF + ions:x_ions string false true,false
OpenPepXLLF + ions:y_ions string true true,false
OpenPepXLLF + ions:z_ions string false true,false
OpenPepXLLF + out_xquest_specxml output-file *.xml,*.spec.xml
OpenPepXLLF + out_xquestxml output-file *.xml,*.xquest.xml
OpenPepXLLF + peptide:enzyme string Trypsin Chymotrypsin/P,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Arg-C,unspecific cleavage,Trypsin,Asp-N/B,Asp-N
OpenPepXLLF + precursor:corrections int
OpenPepXLLF - out_xquest_specxml output-file *.xml
OpenPepXLLF - out_xquestxml output-file *.xml
OpenPepXLLF - peptide:enzyme string Trypsin Arg-C/P,Asp-N,V8-DE,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Lys-C,Lys-N,Asp-N/B,Asp-N_ambic,Chymotrypsin/P,CNBr,Formic_acid,Chymotrypsin,Arg-C,Trypsin,2-iodobenzoate,no cleavage,unspecific cleavage,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase
OpenSwathAnalyzer + algorithm:DIAScoring:dia_extraction_unit string Th Th,ppm
OpenSwathAnalyzer + algorithm:Scores:use_mi_score string false true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms1_mi string false true,false
OpenSwathAnalyzer + algorithm:Scores:use_total_mi_score string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG string false false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:background_subtraction string none none,original,exact
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:boundary_selection_method string largest largest,widest
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_peak_shape_metrics string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_total_mi string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:peak_integration string original original,smoothed
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:use_consensus string true true,false
OpenSwathAnalyzer + algorithm:scoring_model string default default,single_transition
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:background_subtraction string none none,smoothed,original
OpenSwathAssayGenerator + disable_identification_ms2_precursors string false true,false
OpenSwathAssayGenerator + disable_identification_specific_losses string false true,false
OpenSwathAssayGenerator + enable_ipf string false true,false
OpenSwathAssayGenerator + enable_swath_specifity string false true,false
OpenSwathAssayGenerator + in input-file *.tsv,*.mrm,*.pqp,*.TraML
OpenSwathAssayGenerator + in_type string tsv,mrm,pqp,TraML
OpenSwathAssayGenerator + max_num_alternative_localizations int 10000
OpenSwathAssayGenerator + out output-file *.tsv,*.pqp,*.TraML
OpenSwathAssayGenerator + out_type string tsv,pqp,TraML
OpenSwathAssayGenerator + unimod_file input-file *.xml
OpenSwathAssayGenerator - enable_identification_ms2_precursors string false true,false
OpenSwathAssayGenerator - enable_identification_specific_losses string false true,false
OpenSwathAssayGenerator - enable_ms1_uis_scoring string false true,false
OpenSwathAssayGenerator - enable_ms2_uis_scoring string false true,false
OpenSwathAssayGenerator - enable_reannotation string false true,false
OpenSwathAssayGenerator - in input-file *.traML
OpenSwathAssayGenerator - max_num_alternative_localizations int 20
OpenSwathAssayGenerator - out output-file *.traML
OpenSwathChromatogramExtractor + ion_mobility_window double -1
OpenSwathDecoyGenerator + aim_decoy_fraction double 1
OpenSwathDecoyGenerator + in input-file *.tsv,*.mrm,*.pqp,*.TraML
OpenSwathDecoyGenerator + in_type string tsv,mrm,pqp,TraML
OpenSwathDecoyGenerator + method string shuffle shuffle,pseudo-reverse,reverse,shift
OpenSwathDecoyGenerator + min_decoy_fraction double 0.8
OpenSwathDecoyGenerator + out output-file *.tsv,*.pqp,*.TraML
OpenSwathDecoyGenerator + out_type string tsv,pqp,TraML
OpenSwathDecoyGenerator + product_mz_threshold double 0.025
OpenSwathDecoyGenerator + separate string false true,false
OpenSwathDecoyGenerator + shift_precursor_mz_shift double 0
OpenSwathDecoyGenerator + shift_product_mz_shift double 20
OpenSwathDecoyGenerator + shuffle_max_attempts int 30
OpenSwathDecoyGenerator + shuffle_sequence_identity_threshold double 0.5
OpenSwathDecoyGenerator + switchKR string true true,false
OpenSwathDecoyGenerator - append string false true,false
OpenSwathDecoyGenerator - exclude_similar string false true,false
OpenSwathDecoyGenerator - identity_threshold double 0.7
OpenSwathDecoyGenerator - in input-file *.traML
OpenSwathDecoyGenerator - max_attempts int 10
OpenSwathDecoyGenerator - method string shuffle
OpenSwathDecoyGenerator - mz_shift double 20
OpenSwathDecoyGenerator - mz_threshold double 0.05
OpenSwathDecoyGenerator - out output-file *.traML
OpenSwathDecoyGenerator - precursor_mass_shift double 0
OpenSwathDecoyGenerator - remove_CNterm_mods string false true,false
OpenSwathDecoyGenerator - remove_unannotated string false true,false
OpenSwathDecoyGenerator - similarity_threshold double -1
OpenSwathMzMLFileCacher + full_meta string true true,false
OpenSwathMzMLFileCacher + lossy_compression string true true,false
OpenSwathMzMLFileCacher + lossy_mass_accuracy double -1
OpenSwathMzMLFileCacher + lowmem_batchsize int 500 0:
OpenSwathMzMLFileCacher + process_lowmemory string false true,false
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_extraction_unit string Th Th,ppm
OpenSwathRTNormalizer + algorithm:Scores:use_mi_score string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms1_mi string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_total_mi_score string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG string false false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:background_subtraction string none none,original,exact
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:boundary_selection_method string largest largest,widest
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_peak_shape_metrics string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_total_mi string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:peak_integration string original original,smoothed
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:use_consensus string true true,false
OpenSwathRTNormalizer + algorithm:scoring_model string default default,single_transition
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:background_subtraction string none none,smoothed,original
OpenSwathWorkflow + Debugging:irt_mzml string
OpenSwathWorkflow + Debugging:irt_trafo string
OpenSwathWorkflow + Scoring:DIAScoring:dia_extraction_unit string Th Th,ppm
OpenSwathWorkflow + Scoring:Scores:use_mi_score string false true,false
OpenSwathWorkflow + Scoring:Scores:use_ms1_mi string false true,false
OpenSwathWorkflow + Scoring:Scores:use_total_mi_score string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:fit_EMG string false false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid
OpenSwathWorkflow + Scoring:TransitionGroupPicker:background_subtraction string none none,original,exact
OpenSwathWorkflow + Scoring:TransitionGroupPicker:boundary_selection_method string largest largest,widest
OpenSwathWorkflow + Scoring:TransitionGroupPicker:compute_peak_shape_metrics string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:compute_total_mi string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:peak_integration string original original,smoothed
OpenSwathWorkflow + Scoring:TransitionGroupPicker:use_consensus string true true,false
OpenSwathWorkflow + Scoring:scoring_model string default default,single_transition
OpenSwathWorkflow + Scoring:uis_threshold_sn int 0
OpenSwathWorkflow + in input-file *.mzML,*.mzXML,*.sqMass
OpenSwathWorkflow + ion_mobility_window double -1
OpenSwathWorkflow - Scoring:TransitionGroupPicker:background_subtraction string none none,smoothed,original
OpenSwathWorkflow - Scoring:uis_threshold_sn int -1
OpenSwathWorkflow - in input-file *.mzML,*.mzXML
PeptideIndexer + aaa_max int 3 0:10
PeptideIndexer + decoy_string string
PeptideIndexer + enzyme:name string Trypsin Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Arg-C,Asp-N,Trypsin,Lys-C,Lys-N,Lys-C/P,PepsinA,elastase-trypsin-chymotrypsin,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,unspecific cleavage
PeptideIndexer + mismatches_max int 0 0:10
PeptideIndexer + missing_decoy_action string error error,warn,silent
PeptideIndexer - aaa_max int 4 0:
PeptideIndexer - decoy_string string DECOY_
PeptideIndexer - enzyme:name string Trypsin Asp-N/B,Arg-C/P,Trypsin,V8-DE,CNBr,Arg-C,TrypChymo,Lys-N,leukocyte elastase,Alpha-lytic protease,Asp-N_ambic,Chymotrypsin/P,Formic_acid,PepsinA,V8-E,proline endopeptidase,Asp-N,Lys-C,Chymotrypsin,Trypsin/P,Lys-C/P,no cleavage,unspecific cleavage,glutamyl endopeptidase,2-iodobenzoate
PeptideIndexer - filter_aaa_proteins string false true,false
PeptideIndexer - full_tolerant_search string false true,false
PeptideIndexer - mismatches_max int 0 0:
PeptideIndexer - missing_decoy_action string error error,warn
PercolatorAdapter + in_osw input-file *.OSW
PercolatorAdapter + ipf_max_peakgroup_pep double 0.7
PercolatorAdapter + ipf_max_transition_isotope_overlap double 0.5
PercolatorAdapter + ipf_min_transition_sn double 0
PercolatorAdapter + osw_level string ms2
PercolatorAdapter + out output-file *.mzid,*.idXML,*.osw
PercolatorAdapter + out_pin output-file *.tab
PercolatorAdapter + out_type string mzid,idXML,osw
PercolatorAdapter + score_type string q-value q-value,pep,svm
PercolatorAdapter + train-best-positive string false true,false
PercolatorAdapter - mzid_out output-file *.mzid
PercolatorAdapter - out output-file *.idXML
PhosphoScoring + fragment_mass_tolerance double 0.05 0:
PhosphoScoring + max_num_perm int 16384 0:
PhosphoScoring + max_peptide_length int 40 0:
PhosphoScoring + out output-file
PhosphoScoring + unambiguous_score int 1000
PhosphoScoring - fragment_mass_tolerance double 0.05
PhosphoScoring - max_num_perm int 16384 1:
PhosphoScoring - max_peptide_length int 40 1:
PhosphoScoring - out output-file *.idXML
RNPxlSearch + RNPxl:can_cross_link string U
RNPxlSearch + RNPxl:decoys string false true,false
RNPxlSearch + RNPxl:scoring string fast fast,slow
RNPxlSearch + peptide:enzyme string Trypsin Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
RNPxlSearch + peptide:max_size int 1000000
RNPxlSearch - RNPxl:restrictions string
RNPxlSearch - peptide:enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Asp-N,Lys-C,V8-DE,Lys-C/P,PepsinA,V8-E,Asp-N/B,CNBr,proline endopeptidase,unspecific cleavage,Lys-N,2-iodobenzoate,leukocyte elastase,Asp-N_ambic,Formic_acid,Arg-C/P,Arg-C,Chymotrypsin,TrypChymo,Trypsin/P,Trypsin,no cleavage,Chymotrypsin/P
SimpleSearchEngine + enzyme string Trypsin staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,iodosobenzoate,2-iodobenzoate,PepsinA + P,Clostripain/P,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,cyanogen-bromide
SimpleSearchEngine + peptide:motif string
SimpleSearchEngine - enzyme string Trypsin Asp-N/B,V8-E,Chymotrypsin/P,Asp-N_ambic,Lys-C,Alpha-lytic protease,leukocyte elastase,unspecific cleavage,Chymotrypsin,V8-DE,Trypsin,Arg-C,2-iodobenzoate,glutamyl endopeptidase,Lys-N,Lys-C/P,TrypChymo,proline endopeptidase,Asp-N,no cleavage,Formic_acid,CNBr,Arg-C/P,PepsinA,Trypsin/P
SiriusAdapter + compound_timeout int 10
SiriusAdapter + elements string CHNOP[5]S[8]Cl[1]
SiriusAdapter + feature_only string false true,false
SiriusAdapter + filter_by_num_masstraces int 1 1:
SiriusAdapter + in_featureinfo input-file *.featurexml
SiriusAdapter + ion_tree string false true,false
SiriusAdapter + isotope_pattern_iterations int 3
SiriusAdapter + most_intense_ms2 string false true,false
SiriusAdapter + no_masstrace_info_isotope_pattern string false true,false
SiriusAdapter + out_fingerid output-file *.mzTab
SiriusAdapter + out_sirius output-file *.mzTab
SiriusAdapter + precursor_mz_tolerance double 0.005
SiriusAdapter + precursor_mz_tolerance_unit string Da Da,ppm
SiriusAdapter + precursor_rt_tolerance double 5
SiriusAdapter + top_n_hits int 10
SiriusAdapter + tree_timeout int 0
SiriusAdapter - elements string CHNOP[5]S
SiriusAdapter - iontree string false true,false
SiriusAdapter - number int 10
SiriusAdapter - out_fingerid output-file *.tsv
SiriusAdapter - out_sirius output-file *.tsv
SpecLibSearcher + fragment:mass_tolerance double 10
SpecLibSearcher + modifications:fixed string ...
SpecLibSearcher + modifications:variable string ...
SpecLibSearcher + modifications:variable_max_per_peptide int 2
SpecLibSearcher + precursor:isotopes int
SpecLibSearcher + precursor:mass_tolerance double 10
SpecLibSearcher + precursor:mass_tolerance_unit string ppm ppm,Da
SpecLibSearcher + precursor:max_charge int 5
SpecLibSearcher + precursor:min_charge int 2
SpecLibSearcher + report:top_hits int 10
SpecLibSearcher - fixed_modifications string ...
SpecLibSearcher - precursor_mass_tolerance double 3
SpecLibSearcher - round_precursor_to_integer int 10
SpecLibSearcher - top_hits int 10
SpecLibSearcher - variable_modifications string ...
XFDR + decoy_string string DECOY_
XFDR + in input-file *.xml,*.idXML,*.mzid,*.xquest.xml
XFDR + in_type string xml,idXML,mzid,xquest.xml
XFDR + out_xquest output-file *.xquest.xml
XFDR - in input-file *.xml,*.idXML,*.mzid
XFDR - in_type string xml,idXML,mzid
XTandemAdapter + enzyme string Trypsin Trypsin,Arg-C/P,Asp-N_ambic,PepsinA,TrypChymo,Asp-N,Lys-N,Lys-C/P,unspecific cleavage,Lys-C,2-iodobenzoate,Asp-N/B,Arg-C,V8-DE,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase
XTandemAdapter - enzyme string Trypsin glutamyl endopeptidase,Formic_acid,TrypChymo,Arg-C/P,Lys-C,Alpha-lytic protease,2-iodobenzoate,CNBr,leukocyte elastase,unspecific cleavage,Lys-C/P,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Asp-N,V8-E,Lys-N,Asp-N/B,Trypsin,Arg-C,Trypsin/P,PepsinA,V8-DE
------------------------------------------------------------------------------------------
---- OpenMS 2.3 ----
------------------------------------------------------------------------------------------
OpenMS 2.3 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.2 are:
TOPPView:
- Deletion of selections of Peak Annotations is reflected in the Peptide Hit
- Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter
- Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially
New tools:
- CometAdapter -- Annotates MS/MS spectra using Comet (TOPP)
- MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the same metabolite (UTIL)
- OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL)
- OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers (UTIL)
- PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL)
- SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
- XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)
Deprecated and removed tools:
- None
Renamed tool:
- LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess
Major changes in functionality:
- Experimental design
- Add support for fractions
- FeatureLinkerUnlabeledKD
- m/z and retention time tolerances for warping and linking are now separate parameters
- IsobaricAnalyzer
- Support for TMT11plex (https://www.thermofisher.com/order/catalog/product/A34808)
- FileInfo
- For idXML files, the tool computes the average length of contained peptides
- TopPerc
- Renamed in PercolatorAdapter (still experimental)
- OpenSWATH:
- RT normalization now allows more models
- Add S/N ratio for each ion trace
- Support for C++11 (requires a compiler that supports C++11)
Library:
- TOPP tools report their peak memory usage when using -debug 1 (or higher)
- idXML files can now be written faster (about 10%)
- pyOpenMS bindings for DataArrayByName getters
- Python build are now split in compilation units and can thus run in parallel
- FASTA files can now be written
- Allow String values to be passed to EnzymaticDigestion::isValidProduct
File formats:
- consensusXML now supports both channels and MS runs. Information will also be exported in mzTab
Scripts:
- None
Databases:
- None
Third-party software:
- New: Comet "2016.01 rev. 3" for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit
- New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental)
- New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit
- New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit
- Update MS-GF+ to Release (v2017.07.21)
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + negative_adducts input-file CHEMISTRY/NegativeAdducts.tsv *.tsv
AccurateMassSearch + out output-file *.tsv
AccurateMassSearch + positive_adducts input-file CHEMISTRY/PositiveAdducts.tsv *.tsv
AccurateMassSearch - negative_adducts_file input-file CHEMISTRY/NegativeAdducts.tsv *.tsv
AccurateMassSearch - out output-file *.csv
AccurateMassSearch - positive_adducts_file input-file CHEMISTRY/PositiveAdducts.tsv *.tsv
Digestor + enzyme string Trypsin Arg-C/P,glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-N,Chymotrypsin,Asp-N/B,Asp-N_ambic,CNBr,Formic_acid,proline endopeptidase,Lys-C/P,Chymotrypsin/P,Asp-N,Lys-C,Trypsin,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,PepsinA,TrypChymo,Trypsin/P
Digestor - enzyme string Trypsin Asp-N,PepsinA,TrypChymo,Trypsin,Lys-C,Lys-C/P,Asp-N_ambic,Formic_acid,CNBr,Chymotrypsin,Arg-C,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage
DigestorMotif + enzyme string Trypsin Chymotrypsin,CNBr,Asp-N_ambic,Lys-N,2-iodobenzoate,no cleavage,Trypsin/P,V8-DE,Arg-C/P,Formic_acid,Lys-C/P,Lys-C,Arg-C,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase,leukocyte elastase,unspecific cleavage,Asp-N/B,TrypChymo,Asp-N,Chymotrypsin/P,PepsinA,Trypsin
DigestorMotif - enzyme string Trypsin Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,Asp-N,Asp-N_ambic,Chymotrypsin,unspecific cleavage,Arg-C,V8-E,no cleavage,Trypsin,Trypsin/P,V8-DE,CNBr
FeatureFinderMetabo + out_chrom output-file *.mzML
FeatureLinkerUnlabeled + design input-file *.tsv
FeatureLinkerUnlabeledKD + algorithm:link:mz_tol double 10 0:
FeatureLinkerUnlabeledKD + algorithm:link:rt_tol double 30 0:
FeatureLinkerUnlabeledKD + algorithm:warp:enabled string true true,false
FeatureLinkerUnlabeledKD + algorithm:warp:max_nr_conflicts int 0 -1:
FeatureLinkerUnlabeledKD + algorithm:warp:max_pairwise_log_fc double 0.5
FeatureLinkerUnlabeledKD + algorithm:warp:min_rel_cc_size double 0.5 0:1
FeatureLinkerUnlabeledKD + algorithm:warp:mz_tol double 5 0:
FeatureLinkerUnlabeledKD + algorithm:warp:rt_tol double 100 0:
FeatureLinkerUnlabeledKD + design input-file *.tsv
FeatureLinkerUnlabeledKD - algorithm:max_nr_conflicts int 0 -1:
FeatureLinkerUnlabeledKD - algorithm:max_pairwise_log_fc double 0.5
FeatureLinkerUnlabeledKD - algorithm:min_rel_cc_size double 0.5 0:1
FeatureLinkerUnlabeledKD - algorithm:mz_tol double 15 0:
FeatureLinkerUnlabeledKD - algorithm:rt_tol double 60 0:
FeatureLinkerUnlabeledKD - algorithm:warp string true true,false
FeatureLinkerUnlabeledQT + design input-file *.tsv
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML
FileMerger + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML,*.FASTA
FileMerger + in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML,FASTA
FileMerger - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML
FileMerger - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML
IDFileConverter + add_ionmatch_annotation double 0
IDFilter + digest:enzyme string Trypsin unspecific cleavage,PepsinA,Trypsin/P,Lys-N,2-iodobenzoate,no cleavage,glutamyl endopeptidase,Asp-N,Lys-C/P,Lys-C,CNBr,Asp-N_ambic,leukocyte elastase,V8-DE,Arg-C,Trypsin,V8-E,Alpha-lytic protease,proline endopeptidase,Asp-N/B,Arg-C/P,Formic_acid,Chymotrypsin/P,TrypChymo,Chymotrypsin
IDFilter - digest:enzyme string Trypsin proline endopeptidase,2-iodobenzoate,CNBr,Arg-C,Chymotrypsin,Asp-N_ambic,Asp-N,Formic_acid,glutamyl endopeptidase,no cleavage,leukocyte elastase,V8-E,Lys-C/P,unspecific cleavage,TrypChymo,Trypsin/P,Lys-C,Trypsin,V8-DE,PepsinA
IsobaricAnalyzer + tmt11plex:channel_126_description string
IsobaricAnalyzer + tmt11plex:channel_127C_description string
IsobaricAnalyzer + tmt11plex:channel_127N_description string
IsobaricAnalyzer + tmt11plex:channel_128C_description string
IsobaricAnalyzer + tmt11plex:channel_128N_description string
IsobaricAnalyzer + tmt11plex:channel_129C_description string
IsobaricAnalyzer + tmt11plex:channel_129N_description string
IsobaricAnalyzer + tmt11plex:channel_130C_description string
IsobaricAnalyzer + tmt11plex:channel_130N_description string
IsobaricAnalyzer + tmt11plex:channel_131C_description string
IsobaricAnalyzer + tmt11plex:channel_131N_description string
IsobaricAnalyzer + tmt11plex:correction_matrix string
IsobaricAnalyzer + tmt11plex:reference_channel string 126 126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C
IsobaricAnalyzer + type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt6plex
IsobaricAnalyzer - type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt6plex
MRMMapper + allow_multiple_mappings string false true,false
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:method string corrected legacy,corrected,crawdad
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:peak_width double -1
MRMTransitionGroupPicker + algorithm:resample_boundary double 15
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:method string legacy legacy,corrected,crawdad
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:peak_width double 40
MSGFPlusAdapter + enzyme string Trypsin/P Alpha-lytic protease,Arg-C/P,Asp-N/B,Chymotrypsin/P,Lys-C/P,Lys-N,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage
MSGFPlusAdapter + precursor_mass_tolerance double 10
MSGFPlusAdapter - enzyme string trypsin unspecific,trypsin,chymotrypsin,LysC,LysN,GluC,ArgC,AspN,alphaLP,no_cleavage
MSGFPlusAdapter - precursor_mass_tolerance double 20
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin no cleavage,unspecific cleavage,glutamyl endopeptidase,Arg-C,Formic_acid,Asp-N_ambic,Asp-N,Asp-N/B,V8-DE,proline endopeptidase,Alpha-lytic protease,Lys-C,Lys-N,Chymotrypsin,Arg-C/P,CNBr,Chymotrypsin/P,Trypsin,Trypsin/P,V8-E,2-iodobenzoate,leukocyte elastase,Lys-C/P,PepsinA,TrypChymo
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Lys-C,Lys-C/P,Trypsin,CNBr,Formic_acid,Asp-N,Chymotrypsin,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Asp-N_ambic,Arg-C
MapAlignerIdentification + design input-file *.tsv
MyriMatchAdapter + precursor_mass_tolerance double 10
MyriMatchAdapter + precursor_mass_tolerance_unit string ppm Da,ppm
MyriMatchAdapter - precursor_mass_tolerance double 1.5
MyriMatchAdapter - precursor_mass_tolerance_unit string Da Da,ppm
OMSSAAdapter + enzyme string Trypsin Trypsin,Lys-C/P,Lys-C,Arg-C,CNBr,PepsinA,no cleavage,glutamyl endopeptidase,Chymotrypsin,Formic_acid,Asp-N,Asp-N_ambic,Trypsin/P,unspecific cleavage,TrypChymo
OMSSAAdapter + precursor_error_units string ppm Da,ppm
OMSSAAdapter + precursor_mass_tolerance double 10
OMSSAAdapter - enzyme string Trypsin Trypsin,Asp-N_ambic,unspecific cleavage,Chymotrypsin,glutamyl endopeptidase,no cleavage,TrypChymo,Trypsin/P,CNBr,Formic_acid,Arg-C,Asp-N,Lys-C,Lys-C/P,PepsinA
OMSSAAdapter - precursor_mass_tolerance double 1.5
OMSSAAdapter - precursor_mass_tolerance_unit_ppm string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:resample_boundary double 15
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathRTNormalizer + RTNormalization:RANSACMaxIterations int 1000
OpenSwathRTNormalizer + RTNormalization:RANSACMaxPercentRTThreshold int 3
OpenSwathRTNormalizer + RTNormalization:RANSACSamplingSize int 10
OpenSwathRTNormalizer + RTNormalization:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathRTNormalizer + RTNormalization:useIterativeChauvenet string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:resample_boundary double 15
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathRTNormalizer - outlierDetection:RANSACMaxIterations int 1000
OpenSwathRTNormalizer - outlierDetection:RANSACMaxPercentRTThreshold int 3
OpenSwathRTNormalizer - outlierDetection:RANSACSamplingSize int 10
OpenSwathRTNormalizer - outlierDetection:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathRTNormalizer - outlierDetection:useIterativeChauvenet string false true,false
OpenSwathWorkflow + RTNormalization:InitialQualityCutoff double 0.5
OpenSwathWorkflow + RTNormalization:MinBinsFilled int 8
OpenSwathWorkflow + RTNormalization:MinPeptidesPerBin int 1
OpenSwathWorkflow + RTNormalization:NrRTBins int 10
OpenSwathWorkflow + RTNormalization:OverallQualityCutoff double 5.5
OpenSwathWorkflow + RTNormalization:RANSACMaxIterations int 1000
OpenSwathWorkflow + RTNormalization:RANSACMaxPercentRTThreshold int 3
OpenSwathWorkflow + RTNormalization:RANSACSamplingSize int 10
OpenSwathWorkflow + RTNormalization:alignmentMethod string linear linear,interpolated,lowess,b_spline
OpenSwathWorkflow + RTNormalization:b_spline:num_nodes int 5 0:
OpenSwathWorkflow + RTNormalization:estimateBestPeptides string false true,false
OpenSwathWorkflow + RTNormalization:lowess:span double 0.666666666666667 0:1
OpenSwathWorkflow + RTNormalization:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathWorkflow + RTNormalization:useIterativeChauvenet string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:resample_boundary double 15
OpenSwathWorkflow - outlierDetection:InitialQualityCutoff double 0.5
OpenSwathWorkflow - outlierDetection:MinBinsFilled int 8
OpenSwathWorkflow - outlierDetection:MinPeptidesPerBin int 1
OpenSwathWorkflow - outlierDetection:NrRTBins int 10
OpenSwathWorkflow - outlierDetection:OverallQualityCutoff double 5.5
OpenSwathWorkflow - outlierDetection:RANSACMaxIterations int 1000
OpenSwathWorkflow - outlierDetection:RANSACMaxPercentRTThreshold int 3
OpenSwathWorkflow - outlierDetection:RANSACSamplingSize int 10
OpenSwathWorkflow - outlierDetection:estimateBestPeptides string false true,false
OpenSwathWorkflow - outlierDetection:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathWorkflow - outlierDetection:useIterativeChauvenet string false true,false
PeptideIndexer + enzyme:name string Trypsin proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Asp-N_ambic,Asp-N/B,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C/P,Arg-C,Trypsin
PeptideIndexer - enzyme:name string Trypsin Lys-C/P,Trypsin,Formic_acid,Lys-C,Arg-C,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Asp-N,Asp-N_ambic
RNPxlSearch + peptide:enzyme string Trypsin Trypsin,proline endopeptidase,Alpha-lytic protease,Lys-C/P,leukocyte elastase,Chymotrypsin,no cleavage,Chymotrypsin/P,Lys-N,Asp-N_ambic,PepsinA,Arg-C/P,V8-DE,V8-E,Trypsin/P,unspecific cleavage,2-iodobenzoate,CNBr,Formic_acid,Asp-N,Lys-C,Asp-N/B,Arg-C,glutamyl endopeptidase,TrypChymo
RNPxlSearch + precursor:isotopes int
RNPxlSearch - peptide:enzyme string Trypsin Lys-C,Trypsin,Formic_acid,Lys-C/P,PepsinA,glutamyl endopeptidase,no cleavage,Chymotrypsin,CNBr,2-iodobenzoate,leukocyte elastase,proline endopeptidase,Asp-N,Arg-C,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage,Asp-N_ambic
SimpleSearchEngine + enzyme string Trypsin Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,proline endopeptidase,leukocyte elastase,unspecific cleavage,Asp-N/B,Chymotrypsin,Trypsin,Asp-N_ambic,Formic_acid,Lys-N,CNBr,Chymotrypsin/P,Arg-C/P,Asp-N,Lys-C,no cleavage,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,Arg-C
SimpleSearchEngine + precursor:isotopes int
SimpleSearchEngine - enzyme string Trypsin glutamyl endopeptidase,no cleavage,unspecific cleavage,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,Asp-N,Asp-N_ambic,Chymotrypsin,Arg-C,Lys-C/P,PepsinA,CNBr,Formic_acid,Lys-C,Trypsin
XTandemAdapter + enzyme string Trypsin Trypsin/P,Arg-C/P,V8-DE,Formic_acid,Asp-N,Chymotrypsin/P,CNBr,Lys-C/P,unspecific cleavage,Asp-N/B,Lys-C,Chymotrypsin,PepsinA,Lys-N,Trypsin,glutamyl endopeptidase,2-iodobenzoate,leukocyte elastase,Alpha-lytic protease,V8-E,Arg-C,TrypChymo,Asp-N_ambic
XTandemAdapter - enzyme string Trypsin Trypsin,Formic_acid,Lys-C,Chymotrypsin,CNBr,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,glutamyl endopeptidase,unspecific cleavage,Asp-N_ambic,Asp-N,Arg-C
------------------------------------------------------------------------------------------
---- OpenMS 2.2 ----
------------------------------------------------------------------------------------------
OpenMS 2.2 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.1 are:
New tools:
- RNPxlSearch -- Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL)
- SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable (UTIL)
- FeatureLinkerUnlabeledKD -- Feature linking using a KD tree (TOPP)
- DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins (UTIL)
- TargetedFileConverter -- Conversion of multiple targeted file formats (CSV, TraML etc)
Deprecated and removed tools:
- ITRAQAnalyzer -- superseded by IsobaricAanalyzer
- TMTAnalyzer -- superseded by IsobaricAanalyzer
- ConvertTSVToTraML - superseded by TargetedFileConverter
- ConvertTraMLToTSV - superseded by TargetedFileConverter
- MapAlignmentEvaluation -- removed as deprecated
Major changes in functionality:
- OpenSWATH analysis
- Support for metabolomics workflows
- Support for scanning SWATH (SONAR)
- Support for SQL-based file formats
- XTandemAdapter
- Simplified usage
- Improved support for PTMs and newer X! Tandem versions ("Vengeance", "Alanine")
- IsobaricAnalyzer
- Support for TMT10plex
- Support for quantification in MS3 data
- IDMapper
- Allows to map unidentified tandem mass spectra to features
- FeatureFinderIdentification
- Advanced multi-sample support using machine learning
- FileFilter
- Allows users to enable zlib and lossy compression (see "-lossy_compression")
- Allows users to set desired mass accuracy
- IDFilter
- Added option to filter for valid digestion products
- FalseDiscoveryRate
- Allow filtering by q-value in the tool (no need for IDFilter with "score:pep" option)
Library:
- Averagine approximation for fragment isotope distributions
- Precursor mass correction supports correction to highest intensity peak in tolerance window
- Functionality for resampling and adding of spectra
- Protein-protein cross-link spectrum generator
- Terminal modifications are now separated by "." in text output
- SQLite support in OpenSWATH
- TheoreticalSpectrumGenerator speed-up and removal of RichPeak code
- Removal of template parameters from MSExperiment (reduced compile time and binary size)
- Allow estimation of isotope distributions with predefined numbers of sulfur atoms
- Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK)
- Improved handling of terminal and residue specificity of modifications
- Improved annotation of peptide identifications with spectrum references
- Improved handling of unknown amino acids ("X") in sequences
File formats:
- Improved mzML support for SONAR data and mzML with drift time (experimental)
- Improved support for cross-link data and unknown modifications in mzIdentML
- mzXML writer able to write MaxQuant-compatible files
- mzML files now routinely support substantial compression (up to 5x compression, see #2449, #2458)
- Support for Percolator result files based on X! Tandem searches
Scripts:
- New R script for visualizing RT transformations (trafoXML)
Databases:
- By default, decoy sequences are now denoted by the prefix "DECOY_"
Third-party software:
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
DecoyDatabase + only_decoy string false true,false
DecoyDatabase - append string true true,false
Digestor + enzyme string Trypsin CNBr,proline endopeptidase,TrypChymo,no cleavage,V8-E,leukocyte elastase,Trypsin/P,Lys-C,Formic_acid,glutamyl endopeptidase,Lys-C/P,2-iodobenzoate,Trypsin,V8-DE,Chymotrypsin,PepsinA,Asp-N_ambic,unspecific cleavage,Asp-N,Arg-C
Digestor - enzyme string Trypsin Trypsin,V8-E,leukocyte elastase,Lys-C,Asp-N_ambic,no cleavage,unspecific cleavage,Chymotrypsin,Arg-C,V8-DE,Lys-C/P,2-iodobenzoate,proline endopeptidase,glutamyl endopeptidase,CNBr,TrypChymo,Trypsin/P,Asp-N,PepsinA,Formic_acid
DigestorMotif + enzyme string Trypsin Lys-C,leukocyte elastase,Formic_acid,CNBr,2-iodobenzoate,V8-DE,Trypsin,Lys-C/P,PepsinA,unspecific cleavage,TrypChymo,glutamyl endopeptidase,Arg-C,Asp-N,Chymotrypsin,V8-E,no cleavage,proline endopeptidase,Trypsin/P,Asp-N_ambic
DigestorMotif - enzyme string Trypsin PepsinA,glutamyl endopeptidase,Lys-C,Chymotrypsin,unspecific cleavage,CNBr,Lys-C/P,V8-DE,leukocyte elastase,no cleavage,Asp-N_ambic,Trypsin,proline endopeptidase,2-iodobenzoate,TrypChymo,Trypsin/P,V8-E,Asp-N,Arg-C,Formic_acid
FalseDiscoveryRate + FDR:PSM double 1 0:1
FalseDiscoveryRate + FDR:protein double 1 0:1
FalseDiscoveryRate + PSM string true true,false
FalseDiscoveryRate + protein string true true,false
FalseDiscoveryRate - in_decoy input-file *.idXML
FalseDiscoveryRate - in_target input-file *.idXML
FalseDiscoveryRate - peptides_only string false true,false
FalseDiscoveryRate - proteins_only string false true,false
FeatureFinderIdentification + candidates_in input-file *.featureXML
FeatureFinderIdentification + candidates_out output-file *.featureXML
FeatureFinderIdentification + detect:mapping_tolerance double 0 0:
FeatureFinderIdentification + detect:min_peak_width double 0.2 0:
FeatureFinderIdentification + detect:peak_width double 60 0:
FeatureFinderIdentification + detect:signal_to_noise double 0.8 0.1:
FeatureFinderIdentification + extract:isotope_pmin double 0 0:1
FeatureFinderIdentification + extract:n_isotopes int 2 2:
FeatureFinderIdentification + extract:rt_quantile double 0.95 0:1
FeatureFinderIdentification + extract:rt_window double 0 0:
FeatureFinderIdentification + id_ext input-file *.idXML
FeatureFinderIdentification + model:check:min_area double 1 0:
FeatureFinderIdentification + svm:cache_size double 100 1:
FeatureFinderIdentification + svm:epsilon double 0.001 0:
FeatureFinderIdentification + svm:kernel string RBF RBF,linear
FeatureFinderIdentification + svm:log2_C double
FeatureFinderIdentification + svm:log2_gamma double
FeatureFinderIdentification + svm:min_prob double 0 0:1
FeatureFinderIdentification + svm:no_selection string false true,false
FeatureFinderIdentification + svm:no_shrinking string false true,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_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderIdentification + svm:samples int 0 0:
FeatureFinderIdentification + svm:xval int 5 1:
FeatureFinderIdentification + svm:xval_out output-file *.csv
FeatureFinderIdentification - detect:all_features string false true,false
FeatureFinderIdentification - detect:peak_width double 30 0:
FeatureFinderIdentification - extract:isotope_pmin double 0.03 0:1
FeatureFinderIdentification - extract:reference_rt string adapt adapt,score,intensity,median,all
FeatureFinderIdentification - extract:rt_window double 60 0:
FeatureFinderIdentification - trafo_out output-file *.trafoXML
FeatureFinderMultiplex + algorithm:spectrum_type string automatic profile,centroid,automatic
FeatureLinkerUnlabeled + algorithm:distance_intensity:log_transform string disabled enabled,disabled
FeatureLinkerUnlabeledQT + algorithm:distance_intensity:log_transform string disabled enabled,disabled
FeatureLinkerUnlabeledQT + algorithm:nr_partitions int 100 1:
FeatureLinkerUnlabeledQT - algorithm:nr_partitions int 1 1:
FileConverter + force_MaxQuant_compatibility string false true,false
FileConverter + lossy_compression string false true,false
FileConverter + lossy_mass_accuracy double -1
FileConverter + write_scan_index string true true,false
FileConverter - write_mzML_index string false true,false
FileFilter + peak_options:zlib_compression string false true,false
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML
FileInfo + in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid
FileInfo - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid
HighResPrecursorMassCorrector + highest_intensity_peak:mz_tolerance double 0
IDFileConverter + no_spectra_data_override string false true,false
IDFilter + digest:enzyme string Trypsin unspecific cleavage,Arg-C,Trypsin,Formic_acid,proline endopeptidase,TrypChymo,V8-E,Asp-N_ambic,glutamyl endopeptidase,CNBr,PepsinA,2-iodobenzoate,Chymotrypsin,Lys-C/P,Asp-N,Lys-C,Trypsin/P,leukocyte elastase,no cleavage,V8-DE
IDFilter + digest:fasta input-file *.fasta
IDFilter + digest:methionine_cleavage string false true,false
IDFilter + digest:missed_cleavages int -1 -1:
IDFilter + digest:specificity string full full,semi,none
IDMapper + spectra:in input-file *.mzML
IsobaricAnalyzer + extraction:reporter_mass_shift double 0.002 0.0001:0.5
IsobaricAnalyzer - extraction:reporter_mass_shift double 0.1 1e-08:0.5
LowMemPeakPickerHiRes + algorithm:report_FWHM_unit string relative relative,absolute
LowMemPeakPickerHiRes + algorithm:signal_to_noise double 0 0:
LowMemPeakPickerHiRes - algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
LowMemPeakPickerHiRes - algorithm:signal_to_noise double 1 0:
LowMemPeakPickerHiRes_RandomAccess + algorithm:report_FWHM_unit string relative relative,absolute
LowMemPeakPickerHiRes_RandomAccess + algorithm:signal_to_noise double 0 0:
LowMemPeakPickerHiRes_RandomAccess - algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
LowMemPeakPickerHiRes_RandomAccess - algorithm:signal_to_noise double 1 0:
LuciphorAdapter + java_memory int 3500
LuciphorAdapter + java_permgen int 0
MRMTransitionGroupPicker + algorithm:compute_peak_quality string false true,false
MRMTransitionGroupPicker + algorithm:recalculate_peaks string false true,false
MRMTransitionGroupPicker + algorithm:use_precursors string false true,false
MRMTransitionGroupPicker - algorithm:compute_peak_quality string false
MRMTransitionGroupPicker - algorithm:recalculate_peaks string false
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin unspecific cleavage,Lys-C,Formic_acid,no cleavage,Chymotrypsin,V8-DE,glutamyl endopeptidase,V8-E,Trypsin,Asp-N,CNBr,Trypsin/P,TrypChymo,PepsinA,Arg-C,leukocyte elastase,Lys-C/P,proline endopeptidase,Asp-N_ambic,2-iodobenzoate
MSSimulator + algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges string false true,false
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Asp-N,leukocyte elastase,proline endopeptidase,Lys-C,Lys-C/P,V8-DE,Asp-N_ambic,Formic_acid,no cleavage,Chymotrypsin,glutamyl endopeptidase,2-iodobenzoate,CNBr,unspecific cleavage,V8-E,TrypChymo,Arg-C,Trypsin,Trypsin/P,PepsinA
MapAlignerPoseClustering + algorithm:pairfinder:distance_intensity:log_transform string disabled enabled,disabled
MetaboliteSpectralMatcher + database input-file CHEMISTRY/MetaboliteSpectralDB.mzML *.mzML
MetaboliteSpectralMatcher + out output-file *.tsv
MetaboliteSpectralMatcher - out output-file *.csv
OMSSAAdapter + enzyme string Trypsin Trypsin,TrypChymo,Lys-C/P,PepsinA,glutamyl endopeptidase,Asp-N,Lys-C,CNBr,Trypsin/P,Asp-N_ambic,Chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Formic_acid
OMSSAAdapter - enzyme string Trypsin Trypsin,Lys-C/P,CNBr,Lys-C,Chymotrypsin,unspecific cleavage,no cleavage,Trypsin/P,Formic_acid,Asp-N_ambic,TrypChymo,PepsinA,glutamyl endopeptidase,Asp-N,Arg-C
OpenSwathAnalyzer + algorithm:Scores:use_sonar_scores string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_peak_quality string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:recalculate_peaks string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:use_precursors string false true,false
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathMzMLFileCacher + in input-file *.mzML,*.sqMass
OpenSwathMzMLFileCacher + in_type string mzML,sqMass
OpenSwathMzMLFileCacher + out output-file *.mzML,*.sqMass
OpenSwathMzMLFileCacher + out_type string mzML,sqMass
OpenSwathMzMLFileCacher - in input-file *.mzML
OpenSwathMzMLFileCacher - out output-file
OpenSwathRTNormalizer + algorithm:Scores:use_sonar_scores string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_peak_quality string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:recalculate_peaks string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:use_precursors string false true,false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathWorkflow + Library:force_invalid_mods string false true,false
OpenSwathWorkflow + Library:override_group_label_check string false true,false
OpenSwathWorkflow + Library:retentionTimeInterpretation string iRT iRT,seconds,minutes
OpenSwathWorkflow + Scoring:Scores:use_sonar_scores string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:compute_peak_quality string true true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:recalculate_peaks string true true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:use_precursors string false true,false
OpenSwathWorkflow + irt_mz_extraction_window double 0.05
OpenSwathWorkflow + out_chrom output-file *.mzML,*.sqMass
OpenSwathWorkflow + out_osw output-file *.osw
OpenSwathWorkflow + out_tsv output-file *.tsv
OpenSwathWorkflow + ppm_irtwindow string false true,false
OpenSwathWorkflow + readOptions string normal normal,cache,cacheWorkingInMemory,workingInMemory
OpenSwathWorkflow + sonar string false true,false
OpenSwathWorkflow + tr input-file *.traML,*.tsv,*.pqp
OpenSwathWorkflow + tr_type string traML,tsv,pqp
OpenSwathWorkflow - Scoring:TransitionGroupPicker:compute_peak_quality string true
OpenSwathWorkflow - Scoring:TransitionGroupPicker:recalculate_peaks string true
OpenSwathWorkflow - out_chrom output-file *.mzML
OpenSwathWorkflow - out_tsv string
OpenSwathWorkflow - readOptions string normal normal,cache,cacheWorkingInMemory
OpenSwathWorkflow - tr input-file *.traML,*.tsv,*.csv
OpenSwathWorkflow - tr_type string traML,tsv,csv
PeakPickerHiRes + algorithm:report_FWHM_unit string relative relative,absolute
PeakPickerHiRes + algorithm:signal_to_noise double 0 0:
PeakPickerHiRes - algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
PeakPickerHiRes - algorithm:signal_to_noise double 1 0:
PeptideIndexer + enzyme:name string Trypsin V8-E,Chymotrypsin,glutamyl endopeptidase,Formic_acid,proline endopeptidase,Trypsin/P,CNBr,Asp-N_ambic,Asp-N,Arg-C,Lys-C/P,PepsinA,Trypsin,2-iodobenzoate,V8-DE,TrypChymo,unspecific cleavage,no cleavage,leukocyte elastase,Lys-C
PeptideIndexer - enzyme:name string Trypsin Asp-N_ambic,V8-E,Arg-C,CNBr,Formic_acid,Asp-N,no cleavage,leukocyte elastase,proline endopeptidase,Trypsin/P,Trypsin,glutamyl endopeptidase,2-iodobenzoate,V8-DE,PepsinA,Lys-C,unspecific cleavage,Chymotrypsin,Lys-C/P,TrypChymo
RTModel + out_oligo_params output-file *.paramXML
RTModel + out_oligo_trainset output-file *.txt
RTPredict + in_oligo_params input-file *.paramXML
RTPredict + in_oligo_trainset input-file *.txt
SimpleSearchEngine + enzyme string Trypsin TrypChymo,V8-E,2-iodobenzoate,proline endopeptidase,PepsinA,Lys-C,no cleavage,CNBr,leukocyte elastase,Formic_acid,Chymotrypsin,glutamyl endopeptidase,Trypsin/P,Trypsin,unspecific cleavage,Arg-C,Lys-C/P,Asp-N,V8-DE,Asp-N_ambic
SimpleSearchEngine - enzyme string Trypsin Trypsin/P,no cleavage,leukocyte elastase,PepsinA,2-iodobenzoate,Lys-C/P,Lys-C,V8-E,Formic_acid,Chymotrypsin,V8-DE,TrypChymo,unspecific cleavage,Asp-N,proline endopeptidase,Arg-C,Trypsin,CNBr,Asp-N_ambic,glutamyl endopeptidase
XTandemAdapter + default_config_file input-file *.xml
XTandemAdapter + enzyme string Trypsin Asp-N_ambic,V8-E,unspecific cleavage,V8-DE,PepsinA,Trypsin/P,Lys-C,glutamyl endopeptidase,2-iodobenzoate,Lys-C/P,Arg-C,Formic_acid,CNBr,TrypChymo,Chymotrypsin,Asp-N,Trypsin,leukocyte elastase
XTandemAdapter + max_precursor_charge int 4 0:
XTandemAdapter + no_isotope_error string false true,false
XTandemAdapter + xml_out output-file *.xml
XTandemAdapter - allow_isotope_error string yes yes,no
XTandemAdapter - cleavage_site string Trypsin Lys-C/P,CNBr,Arg-C,Chymotrypsin,PepsinA,2-iodobenzoate,Trypsin/P,TrypChymo,V8-DE,Asp-N,Asp-N_ambic,Lys-C,unspecific cleavage,Formic_acid,Trypsin,V8-E,leukocyte elastase,glutamyl endopeptidase
XTandemAdapter - default_config_file input-file CHEMISTRY/XTandem_default_input.xml *.xml
XTandemAdapter - max_precursor_charge int 4
XTandemAdapter - min_precursor_charge int 2
XTandemAdapter - refinement string false true,false
XTandemAdapter - use_noise_suppression string false true,false
------------------------------------------------------------------------------------------
---- OpenMS 2.1 ----
------------------------------------------------------------------------------------------
OpenMS 2.1 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.0.1 are:
New tools:
- ExternalCalibration -- Applies an external mass recalibration (TOPP)
- OpenSwathFileSplitter -- Splits SWATH files into n files, each containing one window (TOPP)
- MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them (UTIL)
- TICCalculator -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking) (UTIL)
Deprecated and removed tools:
- PILISIdentification -- performs a peptide/protein identification with the PILIS engine (TOPP)
- PILISModelCV -- Perform a cross validation of the PILIS model parameters (TOPP)
- PILISModelTrainer -- Train the PILIS model with a given set of spectra and identifications (TOPP)
- PILISSpectraGenerator -- Generate spectra given a list of peptides and a PILIS model (TOPP)
Major changes in functionality:
- Update notification: starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools
online and will print an information message if a newer version is available. This version check occurs only
once per day and tool. Information on which tools are executed will be collected anonymously to identify which
tools are no longer used and to optimally distribute development resources. If the feature causes problems or
concerns, it can be disabled through a command line switch or environment variable (see the documentation).
- InternalCalibration:
- supports calibration using a table of lock masses and peptide ids.
- global or RT-chunked calibration
- linear & quadratic models (with intensity weighting)
- outlier removal via RANSAC
- reoccurring calibrations can be quickly applied to other files using the novel ExternalCalibration tool
- OpenSwathWorkflow
- support for metabolites / small molecules
- MapAlignerIdentification
- support for "lowess" transformation model
- AccurateMassSearch:
- support for multiple databases
- FeatureFinderMetabo
- isotope spacing model for carbon rich molecules (e.g. lipids)
- PeakPickerHiRes and MassTraceExtractor:
- support for FWHM annotation
File formats:
- Improved mzIdentML support (experimental)
- Improved pepXML support
- Improved support for indexed mzML files
- Improved TraML support
Databases:
- By default, decoy sequences are now denoted by a prefix 'DECOY_'.
Third-party software:
- update for 64-bit X!Tandem VENGEANCE (2015.12.15) NOTE: 32-bit version kept at SLEDGEHAMMER (2013.09.01)
- update for MS-GF+ Release v2016.10.14, released October 14, 2016
- update for pwiz 3.0.9935
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + db:mapping input-file *.tsv
AccurateMassSearch + db:struct input-file *.tsv
AccurateMassSearch - db:mapping input-file CHEMISTRY/HMDBMappingFile.tsv *.tsv
AccurateMassSearch - db:struct input-file CHEMISTRY/HMDB2StructMapping.tsv *.tsv
DecoyDatabase + append string true true,false
DecoyDatabase + decoy_string string DECOY_
DecoyDatabase + decoy_string_position string prefix prefix,suffix
DecoyDatabase + method string reverse reverse,shuffle
DecoyDatabase - append string false true,false
DecoyDatabase - decoy_string string _rev
DecoyDatabase - decoy_string_position string suffix prefix,suffix
DecoyDatabase - shuffle string false true,false
FeatureFinderMetabo + algorithm:ffm:isotope_filtering_model string metabolites (5% RMS) metabolites (2% RMS),metabolites (5% RMS),peptides,none
FeatureFinderMetabo + algorithm:ffm:mz_scoring_13C string false false,true
FeatureFinderMetabo + algorithm:ffm:report_convex_hulls string false false,true
FeatureFinderMetabo + algorithm:mtd:quant_method string area area,median
FeatureFinderMetabo - algorithm:ffm:disable_isotope_filtering string false false,true
FeatureFinderMetabo - algorithm:ffm:isotope_model string metabolites metabolites,peptides
FeatureFinderMetabo - algorithm:ffm:isotope_noisemodel string 5%RMS 5%RMS,2%RMS
FeatureFinderMetabo - algorithm:ffm:quant_method string area area,median
FeatureFinderMultiplex + labels:Leu3 double 3.01883 0:
FileConverter + in input-file *.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter + in_type string mzData,mzXML,mzML,cachedMzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
FileConverter + out output-file *.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter + out_type string mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv
FileConverter - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
FileConverter - out output-file *.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter - out_type string mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv
InternalCalibration + RANSAC:enabled string false true,false
InternalCalibration + RANSAC:iter int 70
InternalCalibration + RANSAC:pc_inliers int 30 1:99
InternalCalibration + RANSAC:threshold double 10
InternalCalibration + RT_chunking double 300
InternalCalibration + cal:id_in input-file *.idXML,*.featureXML
InternalCalibration + cal:lock_fail_out output-file *.mzML
InternalCalibration + cal:lock_in input-file *.csv
InternalCalibration + cal:lock_out output-file *.mzML
InternalCalibration + cal:lock_require_iso string false true,false
InternalCalibration + cal:lock_require_mono string false true,false
InternalCalibration + cal:model_type string linear_weighted linear,linear_weighted,quadratic,quadratic_weighted