------------------------------------------------------------------------------------------ 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 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 ------------------------------------------------------------------------------------------