{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.Quzn1SbF/b1/openms_2.6.0+cleaned1-3_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.Quzn1SbF/b2/openms_2.6.0+cleaned1-3_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -2,8 +2,8 @@\n  09492b3ccb638ace8f786fc56ddff8f9 880308 libdevel optional libopenms-dev_2.6.0+cleaned1-3_amd64.deb\n  ccd85a1a320c91047804a49e8286c62a 230656320 debug optional libopenms2.6.0-dbgsym_2.6.0+cleaned1-3_amd64.deb\n  cad7d3cb4d7c17bbbe7a21440ecc6308 8004824 libs optional libopenms2.6.0_2.6.0+cleaned1-3_amd64.deb\n  7c8823ac90482fa1dcfcbf64ed689035 4291440 science optional openms-common_2.6.0+cleaned1-3_all.deb\n  78ae9ae76a5a3e4db93e0e2703d6f293 42967712 doc optional openms-doc_2.6.0+cleaned1-3_all.deb\n  a02db9284ab511463b401504c3cf6c2c 53520 science optional openms_2.6.0+cleaned1-3_all.deb\n  32d5d88738ccb3610cab51835de1ece7 88756244 debug optional topp-dbgsym_2.6.0+cleaned1-3_amd64.deb\n- 37dfec745a2c245396eb9a3991a94bfb 3119656 science optional topp_2.6.0+cleaned1-3_amd64.deb\n+ 07f8e9409364b62fc2dcec7dfd50fd72 3119664 science optional topp_2.6.0+cleaned1-3_amd64.deb\n"}, {"source1": "topp_2.6.0+cleaned1-3_amd64.deb", "source2": "topp_2.6.0+cleaned1-3_amd64.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r--   0        0        0        4 2021-03-02 07:20:17.000000 debian-binary\n--rw-r--r--   0        0        0     6288 2021-03-02 07:20:17.000000 control.tar.xz\n--rw-r--r--   0        0        0  3113176 2021-03-02 07:20:17.000000 data.tar.xz\n+-rw-r--r--   0        0        0     6284 2021-03-02 07:20:17.000000 control.tar.xz\n+-rw-r--r--   0        0        0  3113188 2021-03-02 07:20:17.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -190,15 +190,15 @@\n -rw-r--r--   0 root         (0) root         (0)    38745 2020-10-01 13:46:20.000000 ./usr/share/doc/topp/changelog.gz\n -rw-r--r--   0 root         (0) root         (0)    31665 2021-03-02 07:20:17.000000 ./usr/share/doc/topp/copyright\n drwxr-xr-x   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/lintian/\n drwxr-xr-x   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/lintian/overrides/\n -rw-r--r--   0 root         (0) root         (0)       26 2021-03-02 07:20:17.000000 ./usr/share/lintian/overrides/topp\n drwxr-xr-x   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/man/\n drwxr-xr-x   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/man/man1/\n--rw-r--r--   0 root         (0) root         (0)     5917 2021-03-02 07:20:17.000000 ./usr/share/man/man1/topp.1.gz\n+-rw-r--r--   0 root         (0) root         (0)     5940 2021-03-02 07:20:17.000000 ./usr/share/man/man1/topp.1.gz\n drwxr-xr-x   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/metainfo/\n -rw-r--r--   0 root         (0) root         (0)     1413 2020-10-01 13:46:20.000000 ./usr/share/metainfo/TOPPAS.appdata.xml\n -rw-r--r--   0 root         (0) root         (0)     1709 2020-10-01 13:46:20.000000 ./usr/share/metainfo/TOPPView.appdata.xml\n drwxr-xr-x   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/pixmaps/\n -rw-r--r--   0 root         (0) root         (0)     5833 2021-03-02 07:20:17.000000 ./usr/share/pixmaps/TOPPAS.xpm\n -rw-r--r--   0 root         (0) root         (0)     6142 2021-03-02 07:20:17.000000 ./usr/share/pixmaps/TOPPView.xpm\n lrwxrwxrwx   0 root         (0) root         (0)        0 2021-03-02 07:20:17.000000 ./usr/share/man/man1/AccurateMassSearch.1.gz -> topp.1.gz\n"}, {"source1": "./usr/share/man/man1/topp.1.gz", "source2": "./usr/share/man/man1/topp.1.gz", "unified_diff": null, "details": [{"source1": "topp.1", "source2": "topp.1", "unified_diff": "@@ -16,371 +16,371 @@\n Initiative (PSI) formats for MS data and supports easy integration of\n tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS\n via the TOPPtools concept and a unified parameter handling.\n \n .SH \"AVAILABLE MODULES\"\n \n \n-\\fBAccurateMassSearch\\fR -- Match MS signals to molecules from a database by mass.\n+\\\\fBAccurateMassSearch\\\\fR -- Match MS signals to molecules from a database by mass.\n \n-\\fBAssayGeneratorMetabo\\fR -- Assay library generation from DDA data (Metabolomics).\n+\\\\fBAssayGeneratorMetabo\\\\fR -- Assay library generation from DDA data (Metabolomics).\n \n-\\fBBaselineFilter\\fR -- Removes the baseline from profile spectra using a top-hat filter.\n+\\\\fBBaselineFilter\\\\fR -- Removes the baseline from profile spectra using a top-hat filter.\n \n-\\fBCVInspector\\fR -- A tool for visualization and validation of PSI mapping and CV files.\n+\\\\fBCVInspector\\\\fR -- A tool for visualization and validation of PSI mapping and CV files.\n \n-\\fBClusterMassTraces\\fR -- Creates pseudo spectra.\n+\\\\fBClusterMassTraces\\\\fR -- Creates pseudo spectra.\n \n-\\fBClusterMassTracesByPrecursor\\fR -- Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.\n+\\\\fBClusterMassTracesByPrecursor\\\\fR -- Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.\n \n-\\fBCometAdapter\\fR -- Annotates MS/MS spectra using Comet.\n+\\\\fBCometAdapter\\\\fR -- Annotates MS/MS spectra using Comet.\n \n-\\fBCompNovo\\fR -- Performs a de novo peptide identification using the CompNovo engine.\n+\\\\fBCompNovo\\\\fR -- Performs a de novo peptide identification using the CompNovo engine.\n \n-\\fBCompNovoCID\\fR -- Performs a de novo peptide identification using the CompNovo engine.\n+\\\\fBCompNovoCID\\\\fR -- Performs a de novo peptide identification using the CompNovo engine.\n \n-\\fBConsensusID\\fR -- Computes a consensus of peptide identifications of several identification engines.\n+\\\\fBConsensusID\\\\fR -- Computes a consensus of peptide identifications of several identification engines.\n \n-\\fBConsensusMapNormalizer\\fR -- Normalizes maps of one consensusXML file.\n+\\\\fBConsensusMapNormalizer\\\\fR -- Normalizes maps of one consensusXML file.\n \n-\\fBCruxAdapter\\fR -- Identifies MS/MS spectra using Crux.\n+\\\\fBCruxAdapter\\\\fR -- Identifies MS/MS spectra using Crux.\n \n-\\fBDTAExtractor\\fR -- Extracts spectra of an MS run file to several files in DTA format.\n+\\\\fBDTAExtractor\\\\fR -- Extracts spectra of an MS run file to several files in DTA format.\n \n-\\fBDatabaseFilter\\fR -- Filters a protein database (FASTA format) based on identified proteins.\n+\\\\fBDatabaseFilter\\\\fR -- Filters a protein database (FASTA format) based on identified proteins.\n \n-\\fBDatabaseSuitability\\fR -- Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.\n+\\\\fBDatabaseSuitability\\\\fR -- Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.\n \n-\\fBDeMeanderize\\fR -- Orders the spectra of MALDI spotting plates correctly.\n+\\\\fBDeMeanderize\\\\fR -- Orders the spectra of MALDI spotting plates correctly.\n \n-\\fBDecharger\\fR -- Decharges and merges different feature charge variants of the same peptide.\n+\\\\fBDecharger\\\\fR -- Decharges and merges different feature charge variants of the same peptide.\n \n-\\fBDecoyDatabase\\fR -- Create decoy sequence database from forward sequence database.\n+\\\\fBDecoyDatabase\\\\fR -- Create decoy sequence database from forward sequence database.\n \n-\\fBDigestor\\fR -- Digests a protein database in-silico.\n+\\\\fBDigestor\\\\fR -- Digests a protein database in-silico.\n \n-\\fBDigestorMotif\\fR -- digests a protein database in-silico.\n+\\\\fBDigestorMotif\\\\fR -- digests a protein database in-silico.\n \n-\\fBEICExtractor\\fR -- Extracts intensities from dedicates positions in a LC/MS map.\n+\\\\fBEICExtractor\\\\fR -- Extracts intensities from dedicates positions in a LC/MS map.\n \n-\\fBERPairFinder\\fR -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.\n+\\\\fBERPairFinder\\\\fR -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.\n \n-\\fBEpifany\\fR -- Runs a Bayesian protein inference.\n+\\\\fBEpifany\\\\fR -- Runs a Bayesian protein inference.\n \n-\\fBExecutePipeline\\fR -- Executes workflows created by TOPPAS.\n+\\\\fBExecutePipeline\\\\fR -- Executes workflows created by TOPPAS.\n \n-\\fBExternalCalibration\\fR -- Applies an external mass recalibration.\n+\\\\fBExternalCalibration\\\\fR -- Applies an external mass recalibration.\n \n-\\fBFFEval\\fR -- Evaluation tool for feature detection algorithms.\n+\\\\fBFFEval\\\\fR -- Evaluation tool for feature detection algorithms.\n \n-\\fBFalseDiscoveryRate\\fR -- Estimates the false discovery rate on peptide and protein level using decoy searches.\n+\\\\fBFalseDiscoveryRate\\\\fR -- Estimates the false discovery rate on peptide and protein level using decoy searches.\n \n-\\fBFeatureFinderCentroided\\fR -- Detects two-dimensional features in LC-MS data.\n+\\\\fBFeatureFinderCentroided\\\\fR -- Detects two-dimensional features in LC-MS data.\n \n-\\fBFeatureFinderIdentification\\fR -- Detects features in MS1 data based on peptide identifications.\n+\\\\fBFeatureFinderIdentification\\\\fR -- Detects features in MS1 data based on peptide identifications.\n \n-\\fBFeatureFinderIsotopeWavelet\\fR -- Detects two-dimensional features in LC-MS data.\n+\\\\fBFeatureFinderIsotopeWavelet\\\\fR -- Detects two-dimensional features in LC-MS data.\n \n-\\fBFeatureFinderMRM\\fR -- Detects two-dimensional features in LC-MS data.\n+\\\\fBFeatureFinderMRM\\\\fR -- Detects two-dimensional features in LC-MS data.\n \n-\\fBFeatureFinderMetabo\\fR -- Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.\n+\\\\fBFeatureFinderMetabo\\\\fR -- Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.\n \n-\\fBFeatureFinderMetaboIdent\\fR -- Detects features in MS1 data based on metabolite identifications.\n+\\\\fBFeatureFinderMetaboIdent\\\\fR -- Detects features in MS1 data based on metabolite identifications.\n \n-\\fBFeatureFinderMultiplex\\fR -- Determination of peak ratios in LC-MS data.\n+\\\\fBFeatureFinderMultiplex\\\\fR -- Determination of peak ratios in LC-MS data.\n \n-\\fBFeatureFinderSuperHirn\\fR -- Finds mass spectrometric features in mass spectra.\n+\\\\fBFeatureFinderSuperHirn\\\\fR -- Finds mass spectrometric features in mass spectra.\n \n-\\fBFeatureLinkerLabeled\\fR -- Groups corresponding isotope-labeled features in a feature map.\n+\\\\fBFeatureLinkerLabeled\\\\fR -- Groups corresponding isotope-labeled features in a feature map.\n \n-\\fBFeatureLinkerUnlabeled\\fR -- Groups corresponding features from multiple maps.\n+\\\\fBFeatureLinkerUnlabeled\\\\fR -- Groups corresponding features from multiple maps.\n \n-\\fBFeatureLinkerUnlabeledKD\\fR -- Groups corresponding features from multiple maps.\n+\\\\fBFeatureLinkerUnlabeledKD\\\\fR -- Groups corresponding features from multiple maps.\n \n-\\fBFeatureLinkerUnlabeledQT\\fR -- Groups corresponding features from multiple maps.\n+\\\\fBFeatureLinkerUnlabeledQT\\\\fR -- Groups corresponding features from multiple maps.\n \n-\\fBFidoAdapter\\fR -- Runs the protein inference engine Fido.\n+\\\\fBFidoAdapter\\\\fR -- Runs the protein inference engine Fido.\n \n-\\fBFileConverter\\fR -- Converts between different MS file formats.\n+\\\\fBFileConverter\\\\fR -- Converts between different MS file formats.\n \n-\\fBFileFilter\\fR -- Extracts or manipulates portions of data from peak, feature or consensus-feature files.\n+\\\\fBFileFilter\\\\fR -- Extracts or manipulates portions of data from peak, feature or consensus-feature files.\n \n-\\fBFileInfo\\fR -- Shows basic information about the file, such as data ranges and file type.\n+\\\\fBFileInfo\\\\fR -- Shows basic information about the file, such as data ranges and file type.\n \n-\\fBFileMerger\\fR -- Merges several MS files into one file.\n+\\\\fBFileMerger\\\\fR -- Merges several MS files into one file.\n \n-\\fBFuzzyDiff\\fR -- Compares two files, tolerating numeric differences.\n+\\\\fBFuzzyDiff\\\\fR -- Compares two files, tolerating numeric differences.\n \n-\\fBGNPSExport\\fR -- Tool to export consensus features into MGF format.\n+\\\\fBGNPSExport\\\\fR -- Tool to export consensus features into MGF format.\n \n-\\fBGenericWrapper\\fR -- Allows the generic wrapping of external tools.\n+\\\\fBGenericWrapper\\\\fR -- Allows the generic wrapping of external tools.\n \n-\\fBHighResPrecursorMassCorrector\\fR -- Corrects the precursor mass and charge determined by the instrument software.\n+\\\\fBHighResPrecursorMassCorrector\\\\fR -- Corrects the precursor mass and charge determined by the instrument software.\n \n-\\fBIDConflictResolver\\fR -- Resolves ambiguous annotations of features with peptide identifications.\n+\\\\fBIDConflictResolver\\\\fR -- Resolves ambiguous annotations of features with peptide identifications.\n \n-\\fBIDDecoyProbability\\fR -- Estimates peptide probabilities using a decoy search strategy.\n+\\\\fBIDDecoyProbability\\\\fR -- Estimates peptide probabilities using a decoy search strategy.\n \n-\\fBIDExtractor\\fR -- Extracts 'n' peptides randomly or best 'n' from idXML files.\n+\\\\fBIDExtractor\\\\fR -- Extracts 'n' peptides randomly or best 'n' from idXML files.\n \n-\\fBIDFileConverter\\fR -- Converts identification engine file formats.\n+\\\\fBIDFileConverter\\\\fR -- Converts identification engine file formats.\n \n-\\fBIDFilter\\fR -- Filters results from protein or peptide identification engines based on different criteria.\n+\\\\fBIDFilter\\\\fR -- Filters results from protein or peptide identification engines based on different criteria.\n \n-\\fBIDMapper\\fR -- Assigns protein/peptide identifications to features or consensus features.\n+\\\\fBIDMapper\\\\fR -- Assigns protein/peptide identifications to features or consensus features.\n \n-\\fBIDMassAccuracy\\fR -- Calculates a distribution of the mass error from given mass spectra and IDs.\n+\\\\fBIDMassAccuracy\\\\fR -- Calculates a distribution of the mass error from given mass spectra and IDs.\n \n-\\fBIDMerger\\fR -- Merges several protein/peptide identification files into one file.\n+\\\\fBIDMerger\\\\fR -- Merges several protein/peptide identification files into one file.\n \n-\\fBIDPosteriorErrorProbability\\fR -- Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.\n+\\\\fBIDPosteriorErrorProbability\\\\fR -- Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.\n \n-\\fBIDRTCalibration\\fR -- Can be used to calibrate RTs of peptide hits linearly to standards.\n+\\\\fBIDRTCalibration\\\\fR -- Can be used to calibrate RTs of peptide hits linearly to standards.\n \n-\\fBIDRipper\\fR -- Split protein/peptide identification file into several files according to annotated file origin.\n+\\\\fBIDRipper\\\\fR -- Split protein/peptide identification file into several files according to annotated file origin.\n \n-\\fBIDScoreSwitcher\\fR -- Switches between different scores of peptide or protein hits in identification data.\n+\\\\fBIDScoreSwitcher\\\\fR -- Switches between different scores of peptide or protein hits in identification data.\n \n-\\fBIDSplitter\\fR -- Splits protein/peptide identifications off of annotated data files.\n+\\\\fBIDSplitter\\\\fR -- Splits protein/peptide identifications off of annotated data files.\n \n-\\fBINIFileEditor\\fR -- An editor for OpenMS configuration files.\n+\\\\fBINIFileEditor\\\\fR -- An editor for OpenMS configuration files.\n \n-\\fBINIUpdater\\fR -- Update INI and TOPPAS files to new OpenMS version.\n+\\\\fBINIUpdater\\\\fR -- Update INI and TOPPAS files to new OpenMS version.\n \n-\\fBImageCreator\\fR -- Transforms an LC-MS map into an image.\n+\\\\fBImageCreator\\\\fR -- Transforms an LC-MS map into an image.\n \n-\\fBInclusionExclusionListCreator\\fR -- Creates inclusion and/or exclusion lists.\n+\\\\fBInclusionExclusionListCreator\\\\fR -- Creates inclusion and/or exclusion lists.\n \n-\\fBInspectAdapter\\fR -- Annotates MS/MS spectra using Inspect.\n+\\\\fBInspectAdapter\\\\fR -- Annotates MS/MS spectra using Inspect.\n \n-\\fBInternalCalibration\\fR -- Applies an internal mass recalibration.\n+\\\\fBInternalCalibration\\\\fR -- Applies an internal mass recalibration.\n \n-\\fBIsobaricAnalyzer\\fR -- Calculates isobaric quantitative values for peptides.\n+\\\\fBIsobaricAnalyzer\\\\fR -- Calculates isobaric quantitative values for peptides.\n \n-\\fBLabeledEval\\fR -- Evaluation tool for isotope-labeled quantitation experiments.\n+\\\\fBLabeledEval\\\\fR -- Evaluation tool for isotope-labeled quantitation experiments.\n \n-\\fBLuciphorAdapter\\fR -- Modification site localisation using LuciPHOr2.\n+\\\\fBLuciphorAdapter\\\\fR -- Modification site localisation using LuciPHOr2.\n \n-\\fBMRMMapper\\fR -- MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).\n+\\\\fBMRMMapper\\\\fR -- MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).\n \n-\\fBMRMPairFinder\\fR -- Util which can be used to evaluate labeled pair ratios on MRM features.\n+\\\\fBMRMPairFinder\\\\fR -- Util which can be used to evaluate labeled pair ratios on MRM features.\n \n-\\fBMRMTransitionGroupPicker\\fR -- Picks peaks in SRM/MRM chromatograms.\n+\\\\fBMRMTransitionGroupPicker\\\\fR -- Picks peaks in SRM/MRM chromatograms.\n \n-\\fBMSFraggerAdapter\\fR -- Peptide Identification with MSFragger.\n+\\\\fBMSFraggerAdapter\\\\fR -- Peptide Identification with MSFragger.\n \n-\\fBMSGFPlusAdapter\\fR -- MS/MS database search using MS-GF+.\n+\\\\fBMSGFPlusAdapter\\\\fR -- MS/MS database search using MS-GF+.\n \n-\\fBMSSimulator\\fR -- A highly configurable simulator for mass spectrometry experiments.\n+\\\\fBMSSimulator\\\\fR -- A highly configurable simulator for mass spectrometry experiments.\n \n-\\fBMSstatsConverter\\fR -- Converter to input for MSstats.\n+\\\\fBMSstatsConverter\\\\fR -- Converter to input for MSstats.\n \n-\\fBMaRaClusterAdapter\\fR -- Facilitate input to MaRaCluster and reintegrate.\n+\\\\fBMaRaClusterAdapter\\\\fR -- Facilitate input to MaRaCluster and reintegrate.\n \n-\\fBMapAlignerIdentification\\fR -- Corrects retention time distortions between maps based on common peptide identifications.\n+\\\\fBMapAlignerIdentification\\\\fR -- Corrects retention time distortions between maps based on common peptide identifications.\n \n-\\fBMapAlignerPoseClustering\\fR -- Corrects retention time distortions between maps using a pose clustering approach.\n+\\\\fBMapAlignerPoseClustering\\\\fR -- Corrects retention time distortions between maps using a pose clustering approach.\n \n-\\fBMapAlignerSpectrum\\fR -- Corrects retention time distortions between maps by spectrum alignment.\n+\\\\fBMapAlignerSpectrum\\\\fR -- Corrects retention time distortions between maps by spectrum alignment.\n \n-\\fBMapAlignerTreeGuided\\fR -- Tree guided correction of retention time distortions between maps.\n+\\\\fBMapAlignerTreeGuided\\\\fR -- Tree guided correction of retention time distortions between maps.\n \n-\\fBMapNormalizer\\fR -- Normalizes peak intensities in an MS run.\n+\\\\fBMapNormalizer\\\\fR -- Normalizes peak intensities in an MS run.\n \n-\\fBMapRTTransformer\\fR -- Applies retention time transformations to maps.\n+\\\\fBMapRTTransformer\\\\fR -- Applies retention time transformations to maps.\n \n-\\fBMapStatistics\\fR -- Extract extended statistics on the features of a map for quality control.\n+\\\\fBMapStatistics\\\\fR -- Extract extended statistics on the features of a map for quality control.\n \n-\\fBMascotAdapter\\fR -- Annotates MS/MS spectra using Mascot.\n+\\\\fBMascotAdapter\\\\fR -- Annotates MS/MS spectra using Mascot.\n \n-\\fBMascotAdapterOnline\\fR -- Annotates MS/MS spectra using Mascot.\n+\\\\fBMascotAdapterOnline\\\\fR -- Annotates MS/MS spectra using Mascot.\n \n-\\fBMassCalculator\\fR -- Calculates masses and mass-to-charge ratios of peptide sequences.\n+\\\\fBMassCalculator\\\\fR -- Calculates masses and mass-to-charge ratios of peptide sequences.\n \n-\\fBMassTraceExtractor\\fR -- Detects mass traces in centroided LC-MS data.\n+\\\\fBMassTraceExtractor\\\\fR -- Detects mass traces in centroided LC-MS data.\n \n-\\fBMetaProSIP\\fR -- Performs proteinSIP on peptide features for elemental flux analysis.\n+\\\\fBMetaProSIP\\\\fR -- Performs proteinSIP on peptide features for elemental flux analysis.\n \n-\\fBMetaboliteAdductDecharger\\fR -- Decharges and merges different feature charge variants of the same metabolite.\n+\\\\fBMetaboliteAdductDecharger\\\\fR -- Decharges and merges different feature charge variants of the same metabolite.\n \n-\\fBMetaboliteSpectralMatcher\\fR -- Perform a spectral library search.\n+\\\\fBMetaboliteSpectralMatcher\\\\fR -- Perform a spectral library search.\n \n-\\fBMultiplexResolver\\fR -- Completes peptide multiplets and resolves conflicts within them.\n+\\\\fBMultiplexResolver\\\\fR -- Completes peptide multiplets and resolves conflicts within them.\n \n-\\fBMyriMatchAdapter\\fR -- Annotates MS/MS spectra using MyriMatch.\n+\\\\fBMyriMatchAdapter\\\\fR -- Annotates MS/MS spectra using MyriMatch.\n \n-\\fBMzMLSplitter\\fR -- Splits an mzML file into multiple parts.\n+\\\\fBMzMLSplitter\\\\fR -- Splits an mzML file into multiple parts.\n \n-\\fBMzTabExporter\\fR -- Exports various XML formats to an mzTab file.\n+\\\\fBMzTabExporter\\\\fR -- Exports various XML formats to an mzTab file.\n \n-\\fBNoiseFilterGaussian\\fR -- Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).\n+\\\\fBNoiseFilterGaussian\\\\fR -- Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).\n \n-\\fBNoiseFilterSGolay\\fR -- Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.\n+\\\\fBNoiseFilterSGolay\\\\fR -- Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.\n \n-\\fBNovorAdapter\\fR -- Template for Tool creation.\n+\\\\fBNovorAdapter\\\\fR -- Template for Tool creation.\n \n-\\fBNucleicAcidSearchEngine\\fR -- Annotate nucleic acid identifications to MS/MS spectra.\n+\\\\fBNucleicAcidSearchEngine\\\\fR -- Annotate nucleic acid identifications to MS/MS spectra.\n \n-\\fBOMSSAAdapter\\fR -- Annotates MS/MS spectra using OMSSA.\n+\\\\fBOMSSAAdapter\\\\fR -- Annotates MS/MS spectra using OMSSA.\n \n \n \n-\\fBOpenPepXL\\fR -- Tool for protein-protein cross-linking identification using labeled linkers.\n+\\\\fBOpenPepXL\\\\fR -- Tool for protein-protein cross-linking identification using labeled linkers.\n \n-\\fBOpenPepXLLF\\fR -- Tool for protein-protein cross linking with label-free linkers.\n+\\\\fBOpenPepXLLF\\\\fR -- Tool for protein-protein cross linking with label-free linkers.\n \n-\\fBOpenSwathAnalyzer\\fR -- Picks peaks and finds features in an SWATH-MS or SRM experiment.\n+\\\\fBOpenSwathAnalyzer\\\\fR -- Picks peaks and finds features in an SWATH-MS or SRM experiment.\n \n-\\fBOpenSwathAssayGenerator\\fR -- Generates assays according to different models for a specific TraML.\n+\\\\fBOpenSwathAssayGenerator\\\\fR -- Generates assays according to different models for a specific TraML.\n \n-\\fBOpenSwathChromatogramExtractor\\fR -- Extract chromatograms (XIC) from a MS2 map file.\n+\\\\fBOpenSwathChromatogramExtractor\\\\fR -- Extract chromatograms (XIC) from a MS2 map file.\n \n-\\fBOpenSwathConfidenceScoring\\fR -- Compute confidence scores for OpenSwath results.\n+\\\\fBOpenSwathConfidenceScoring\\\\fR -- Compute confidence scores for OpenSwath results.\n \n-\\fBOpenSwathDIAPreScoring\\fR -- Scoring spectra using the DIA scores.\n+\\\\fBOpenSwathDIAPreScoring\\\\fR -- Scoring spectra using the DIA scores.\n \n-\\fBOpenSwathDecoyGenerator\\fR -- Generates decoys according to different models for a specific TraML.\n+\\\\fBOpenSwathDecoyGenerator\\\\fR -- Generates decoys according to different models for a specific TraML.\n \n-\\fBOpenSwathFeatureXMLToTSV\\fR -- Converts a featureXML to a mProphet tsv.\n+\\\\fBOpenSwathFeatureXMLToTSV\\\\fR -- Converts a featureXML to a mProphet tsv.\n \n-\\fBOpenSwathFileSplitter\\fR -- Splits SWATH files into n files, each containing one window.\n+\\\\fBOpenSwathFileSplitter\\\\fR -- Splits SWATH files into n files, each containing one window.\n \n-\\fBOpenSwathMzMLFileCacher\\fR -- This tool caches the spectra and chromatogram data of an mzML to disk.\n+\\\\fBOpenSwathMzMLFileCacher\\\\fR -- This tool caches the spectra and chromatogram data of an mzML to disk.\n \n-\\fBOpenSwathRTNormalizer\\fR -- This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.\n+\\\\fBOpenSwathRTNormalizer\\\\fR -- This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.\n \n-\\fBOpenSwathRewriteToFeatureXML\\fR -- Combines featureXML and mProphet tsv to FDR filtered featureXML.\n+\\\\fBOpenSwathRewriteToFeatureXML\\\\fR -- Combines featureXML and mProphet tsv to FDR filtered featureXML.\n \n-\\fBOpenSwathWorkflow\\fR -- Complete workflow to run OpenSWATH.\n+\\\\fBOpenSwathWorkflow\\\\fR -- Complete workflow to run OpenSWATH.\n \n-\\fBPSMFeatureExtractor\\fR -- Computes extra features for each input PSM.\n+\\\\fBPSMFeatureExtractor\\\\fR -- Computes extra features for each input PSM.\n \n-\\fBPTModel\\fR -- Trains a model for the prediction of proteotypic peptides from a training set.\n+\\\\fBPTModel\\\\fR -- Trains a model for the prediction of proteotypic peptides from a training set.\n \n-\\fBPTPredict\\fR -- predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel.\n+\\\\fBPTPredict\\\\fR -- predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel.\n \n-\\fBPeakPickerHiRes\\fR -- Finds mass spectrometric peaks in profile mass spectra.\n+\\\\fBPeakPickerHiRes\\\\fR -- Finds mass spectrometric peaks in profile mass spectra.\n \n-\\fBPeakPickerIterative\\fR -- Finds mass spectrometric peaks in profile mass spectra.\n+\\\\fBPeakPickerIterative\\\\fR -- Finds mass spectrometric peaks in profile mass spectra.\n \n-\\fBPeakPickerWavelet\\fR -- Finds mass spectrometric peaks in profile mass spectra.\n+\\\\fBPeakPickerWavelet\\\\fR -- Finds mass spectrometric peaks in profile mass spectra.\n \n-\\fBPepNovoAdapter\\fR -- Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.\n+\\\\fBPepNovoAdapter\\\\fR -- Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.\n \n-\\fBPeptideIndexer\\fR -- Refreshes the protein references for all peptide hits.\n+\\\\fBPeptideIndexer\\\\fR -- Refreshes the protein references for all peptide hits.\n \n-\\fBPercolatorAdapter\\fR -- Facilitate input to Percolator and reintegrate.\n+\\\\fBPercolatorAdapter\\\\fR -- Facilitate input to Percolator and reintegrate.\n \n-\\fBPhosphoScoring\\fR -- Scores potential phosphorylation sites in order to localize the most probable sites.\n+\\\\fBPhosphoScoring\\\\fR -- Scores potential phosphorylation sites in order to localize the most probable sites.\n \n-\\fBPrecursorIonSelector\\fR -- PrecursorIonSelector.\n+\\\\fBPrecursorIonSelector\\\\fR -- PrecursorIonSelector.\n \n-\\fBPrecursorMassCorrector\\fR -- Corrects the precursor entries of MS/MS spectra, by using MS1 information.\n+\\\\fBPrecursorMassCorrector\\\\fR -- Corrects the precursor entries of MS/MS spectra, by using MS1 information.\n \n-\\fBProteinInference\\fR -- Protein inference based on an aggregation of the scores of the identified peptides.\n+\\\\fBProteinInference\\\\fR -- Protein inference based on an aggregation of the scores of the identified peptides.\n \n-\\fBProteinQuantifier\\fR -- Compute peptide and protein abundances.\n+\\\\fBProteinQuantifier\\\\fR -- Compute peptide and protein abundances.\n \n-\\fBProteinResolver\\fR -- protein inference.\n+\\\\fBProteinResolver\\\\fR -- protein inference.\n \n-\\fBProteomicsLFQ\\fR -- A standard proteomics LFQ pipeline.\n+\\\\fBProteomicsLFQ\\\\fR -- A standard proteomics LFQ pipeline.\n \n-\\fBQCCalculator\\fR -- Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.\n+\\\\fBQCCalculator\\\\fR -- Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.\n \n-\\fBQCEmbedder\\fR -- Attaches a table or an image to a given qc parameter.\n+\\\\fBQCEmbedder\\\\fR -- Attaches a table or an image to a given qc parameter.\n \n-\\fBQCExporter\\fR -- Will extract several qp from several run/sets in a tabular format.\n+\\\\fBQCExporter\\\\fR -- Will extract several qp from several run/sets in a tabular format.\n \n-\\fBQCExtractor\\fR -- Extracts a table attachment to a given qc parameter.\n+\\\\fBQCExtractor\\\\fR -- Extracts a table attachment to a given qc parameter.\n \n-\\fBQCImporter\\fR -- Imports tables with quality control parameters into qcml files.\n+\\\\fBQCImporter\\\\fR -- Imports tables with quality control parameters into qcml files.\n \n-\\fBQCMerger\\fR -- Merges two qcml files together.\n+\\\\fBQCMerger\\\\fR -- Merges two qcml files together.\n \n-\\fBQCShrinker\\fR -- This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.\n+\\\\fBQCShrinker\\\\fR -- This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.\n \n-\\fBQualityControl\\fR -- Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.\n+\\\\fBQualityControl\\\\fR -- Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.\n \n-\\fBRNADigestor\\fR -- Digests an RNA sequence database in-silico.\n+\\\\fBRNADigestor\\\\fR -- Digests an RNA sequence database in-silico.\n \n-\\fBRNAMassCalculator\\fR -- Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences.\n+\\\\fBRNAMassCalculator\\\\fR -- Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences.\n \n-\\fBRNPxlSearch\\fR -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra.\n+\\\\fBRNPxlSearch\\\\fR -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra.\n \n-\\fBRNPxlXICFilter\\fR -- Remove MS2 spectra from treatment based on the fold change between control and treatment.\n+\\\\fBRNPxlXICFilter\\\\fR -- Remove MS2 spectra from treatment based on the fold change between control and treatment.\n \n-\\fBRTEvaluation\\fR -- Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.\n+\\\\fBRTEvaluation\\\\fR -- Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.\n \n-\\fBRTModel\\fR -- Trains a model for the retention time prediction of peptides from a training set.\n+\\\\fBRTModel\\\\fR -- Trains a model for the retention time prediction of peptides from a training set.\n \n-\\fBRTPredict\\fR -- Predicts retention times for peptides using a model trained by RTModel.\n+\\\\fBRTPredict\\\\fR -- Predicts retention times for peptides using a model trained by RTModel.\n \n-\\fBResampler\\fR -- Transforms an LC/MS map into a resampled map or a PNG image.\n+\\\\fBResampler\\\\fR -- Transforms an LC/MS map into a resampled map or a PNG image.\n \n-\\fBSeedListGenerator\\fR -- Generates seed lists for feature detection.\n+\\\\fBSeedListGenerator\\\\fR -- Generates seed lists for feature detection.\n \n-\\fBSemanticValidator\\fR -- SemanticValidator for semantically validating certain XML files.\n+\\\\fBSemanticValidator\\\\fR -- SemanticValidator for semantically validating certain XML files.\n \n-\\fBSequenceCoverageCalculator\\fR -- Prints information about idXML files.\n+\\\\fBSequenceCoverageCalculator\\\\fR -- Prints information about idXML files.\n \n-\\fBSimpleSearchEngine\\fR -- Annotates MS/MS spectra using SimpleSearchEngine.\n+\\\\fBSimpleSearchEngine\\\\fR -- Annotates MS/MS spectra using SimpleSearchEngine.\n \n-\\fBSiriusAdapter\\fR -- Tool for metabolite identification using single and tandem mass spectrometry.\n+\\\\fBSiriusAdapter\\\\fR -- Tool for metabolite identification using single and tandem mass spectrometry.\n \n-\\fBSpecLibCreator\\fR -- Creates an MSP formatted spectral library.\n+\\\\fBSpecLibCreator\\\\fR -- Creates an MSP formatted spectral library.\n \n-\\fBSpecLibSearcher\\fR -- Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.\n+\\\\fBSpecLibSearcher\\\\fR -- Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.\n \n-\\fBSpectraFilterBernNorm\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterBernNorm\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterMarkerMower\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterMarkerMower\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterNLargest\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterNLargest\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterNormalizer\\fR -- Normalizes intensity of peak spectra.\n+\\\\fBSpectraFilterNormalizer\\\\fR -- Normalizes intensity of peak spectra.\n \n-\\fBSpectraFilterParentPeakMower\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterParentPeakMower\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterScaler\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterScaler\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterSqrtMower\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterSqrtMower\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterThresholdMower\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterThresholdMower\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraFilterWindowMower\\fR -- Applies thresholdfilter to peak spectra.\n+\\\\fBSpectraFilterWindowMower\\\\fR -- Applies thresholdfilter to peak spectra.\n \n-\\fBSpectraMerger\\fR -- Merges spectra (each MS level separately), increasing S/N ratios.\n+\\\\fBSpectraMerger\\\\fR -- Merges spectra (each MS level separately), increasing S/N ratios.\n \n-\\fBSpectraSTSearchAdapter\\fR -- Interface to the SEARCH Mode of the SpectraST executable.\n+\\\\fBSpectraSTSearchAdapter\\\\fR -- Interface to the SEARCH Mode of the SpectraST executable.\n \n-\\fBStaticModification\\fR -- Applies a set of modifications to all PeptideIDs in an idXML file.\n+\\\\fBStaticModification\\\\fR -- Applies a set of modifications to all PeptideIDs in an idXML file.\n \n-\\fBSvmTheoreticalSpectrumGeneratorTrainer\\fR -- Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator.\n+\\\\fBSvmTheoreticalSpectrumGeneratorTrainer\\\\fR -- Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator.\n \n-\\fBSwathWizard\\fR -- An assistant for Swath-Analysis.\n+\\\\fBSwathWizard\\\\fR -- An assistant for Swath-Analysis.\n \n-\\fBTICCalculator\\fR -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).\n+\\\\fBTICCalculator\\\\fR -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).\n \n-\\fBTOFCalibration\\fR -- Applies time of flight calibration.\n+\\\\fBTOFCalibration\\\\fR -- Applies time of flight calibration.\n \n-\\fBTOPPAS\\fR -- An assistant for GUI-driven TOPP workflow design.\n+\\\\fBTOPPAS\\\\fR -- An assistant for GUI-driven TOPP workflow design.\n \n-\\fBTOPPView\\fR -- A viewer for mass spectrometry data.\n+\\\\fBTOPPView\\\\fR -- A viewer for mass spectrometry data.\n \n-\\fBTargetedFileConverter\\fR -- Converts different transition files for targeted proteomics / metabolomics analysis.\n+\\\\fBTargetedFileConverter\\\\fR -- Converts different transition files for targeted proteomics / metabolomics analysis.\n \n-\\fBTextExporter\\fR -- Exports various XML formats to a text file.\n+\\\\fBTextExporter\\\\fR -- Exports various XML formats to a text file.\n \n-\\fBTransformationEvaluation\\fR -- Applies a transformation to a range of values.\n+\\\\fBTransformationEvaluation\\\\fR -- Applies a transformation to a range of values.\n \n-\\fBXFDR\\fR -- Calculates false discovery rate estimates on crosslink identifications.\n+\\\\fBXFDR\\\\fR -- Calculates false discovery rate estimates on crosslink identifications.\n \n-\\fBXMLValidator\\fR -- Validates XML files against an XSD schema.\n+\\\\fBXMLValidator\\\\fR -- Validates XML files against an XSD schema.\n \n-\\fBXTandemAdapter\\fR -- Annotates MS/MS spectra using X! Tandem.\n+\\\\fBXTandemAdapter\\\\fR -- Annotates MS/MS spectra using X! Tandem.\n \n \n .SH \"BIBLIOGRAPHICAL REFERENCE TO BE CITED\"\n Marc Sturm, Andreas Bertsch, Clemens Gr\u00f6pl, Andreas Hildebrandt, Rene\n Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra\n Zerck, Knut Reinert, and Oliver Kohlbacher (2008)  OpenMS \u2013 an\n Open-Source Software Framework for Mass Spectrometry. \\fI BMC\n"}]}]}]}]}]}