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