NAME

       topp - library for LC/MS data management and analysis - tools

DESCRIPTION

       This  manual  page documents briefly the topp package that brings a set of binary tools to
       build the OpenMS proteomics pipeline (topp).  OpenMS  offers  an  infrastructure  for  the
       development  of  mass  spectrometry-related  software and powerful 2D and 3D visualization
       solutions. OpenMS offers analyses for various quantitation protocols, including label-free
       quantitation,  SILAC,  iTRAQ,  SRM,  SWATH…  It  provides  build-in algorithms for de-novo
       identification and database search, as well as adapters to other  state-of-the  art  tools
       like  X!Tandem,  Mascot,  OMSSA…  OpenMS supports the Proteomics Standard 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.

AVAILABLE MODULES

       AccurateMassSearch -- Match MS signals to molecules from a database by mass.

       AssayGeneratorMetabo -- Assay library generation from DDA data (Metabolomics).

       BaselineFilter -- Removes the baseline from profile spectra using a top-hat filter.

       CVInspector -- A tool for visualization and validation of PSI mapping and CV files.

       ClusterMassTraces -- Creates pseudo spectra.

       ClusterMassTracesByPrecursor  --  Correlate  precursor  masstraces   with   fragment   ion
       masstraces in SWATH maps based on their elution profile.

       CometAdapter -- Annotates MS/MS spectra using Comet.

       CompNovo -- Performs a de novo peptide identification using the CompNovo engine.

       CompNovoCID -- Performs a de novo peptide identification using the CompNovo engine.

       ConsensusID  --  Computes a consensus of peptide identifications of several identification
       engines.

       ConsensusMapNormalizer -- Normalizes maps of one consensusXML file.

       CruxAdapter -- Identifies MS/MS spectra using Crux.

       DTAExtractor -- Extracts spectra of an MS run file to several files in DTA format.

       DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins.

       DatabaseSuitability -- Computes a suitability score for a database which was  used  for  a
       peptide identification search. Also reports the quality of LC-MS spectra.

       DeMeanderize -- Orders the spectra of MALDI spotting plates correctly.

       Decharger -- Decharges and merges different feature charge variants of the same peptide.

       DecoyDatabase -- Create decoy sequence database from forward sequence database.

       Digestor -- Digests a protein database in-silico.

       DigestorMotif -- digests a protein database in-silico.

       EICExtractor -- Extracts intensities from dedicates positions in a LC/MS map.

       ERPairFinder  --  Util  which  can  be used to evaluate pair ratios on enhanced resolution
       (zoom) scans.

       Epifany -- Runs a Bayesian protein inference.

       ExecutePipeline -- Executes workflows created by TOPPAS.

       ExternalCalibration -- Applies an external mass recalibration.

       FFEval -- Evaluation tool for feature detection algorithms.

       FalseDiscoveryRate -- Estimates the false discovery rate  on  peptide  and  protein  level
       using decoy searches.

       FeatureFinderCentroided -- Detects two-dimensional features in LC-MS data.

       FeatureFinderIdentification   --   Detects   features   in   MS1  data  based  on  peptide
       identifications.

       FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data.

       FeatureFinderMRM -- Detects two-dimensional features in LC-MS data.

       FeatureFinderMetabo -- Assembles metabolite features from centroided  (LC-)MS  data  using
       the mass trace approach.

       FeatureFinderMetaboIdent   --   Detects   features   in   MS1  data  based  on  metabolite
       identifications.

       FeatureFinderMultiplex -- Determination of peak ratios in LC-MS data.

       FeatureFinderSuperHirn -- Finds mass spectrometric features in mass spectra.

       FeatureLinkerLabeled -- Groups corresponding isotope-labeled features in a feature map.

       FeatureLinkerUnlabeled -- Groups corresponding features from multiple maps.

       FeatureLinkerUnlabeledKD -- Groups corresponding features from multiple maps.

       FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple maps.

       FidoAdapter -- Runs the protein inference engine Fido.

       FileConverter -- Converts between different MS file formats.

       FileFilter -- Extracts or manipulates portions of data from peak,  feature  or  consensus-
       feature files.

       FileInfo -- Shows basic information about the file, such as data ranges and file type.

       FileMerger -- Merges several MS files into one file.

       FuzzyDiff -- Compares two files, tolerating numeric differences.

       GNPSExport -- Tool to export consensus features into MGF format.

       GenericWrapper -- Allows the generic wrapping of external tools.

       HighResPrecursorMassCorrector  -- Corrects the precursor mass and charge determined by the
       instrument software.

       IDConflictResolver  --  Resolves  ambiguous   annotations   of   features   with   peptide
       identifications.

       IDDecoyProbability -- Estimates peptide probabilities using a decoy search strategy.

       IDExtractor -- Extracts 'n' peptides randomly or best 'n' from idXML files.

       IDFileConverter -- Converts identification engine file formats.

       IDFilter  --  Filters  results  from  protein  or  peptide identification engines based on
       different criteria.

       IDMapper -- Assigns protein/peptide identifications to features or consensus features.

       IDMassAccuracy -- Calculates a distribution of the mass error from given mass spectra  and
       IDs.

       IDMerger -- Merges several protein/peptide identification files into one file.

       IDPosteriorErrorProbability  --  Estimates  probabilities for incorrectly assigned peptide
       sequences and a set of search engine scores using a mixture model.

       IDRTCalibration -- Can be used to calibrate RTs of peptide hits linearly to standards.

       IDRipper -- Split protein/peptide identification file  into  several  files  according  to
       annotated file origin.

       IDScoreSwitcher  --  Switches  between  different  scores  of  peptide  or protein hits in
       identification data.

       IDSplitter -- Splits protein/peptide identifications off of annotated data files.

       INIFileEditor -- An editor for OpenMS configuration files.

       INIUpdater -- Update INI and TOPPAS files to new OpenMS version.

       ImageCreator -- Transforms an LC-MS map into an image.

       InclusionExclusionListCreator -- Creates inclusion and/or exclusion lists.

       InspectAdapter -- Annotates MS/MS spectra using Inspect.

       InternalCalibration -- Applies an internal mass recalibration.

       IsobaricAnalyzer -- Calculates isobaric quantitative values for peptides.

       LabeledEval -- Evaluation tool for isotope-labeled quantitation experiments.

       LuciphorAdapter -- Modification site localisation using LuciPHOr2.

       MRMMapper -- MRMMapper  maps  measured  chromatograms  (mzML)  and  the  transitions  used
       (TraML).

       MRMPairFinder -- Util which can be used to evaluate labeled pair ratios on MRM features.

       MRMTransitionGroupPicker -- Picks peaks in SRM/MRM chromatograms.

       MSFraggerAdapter -- Peptide Identification with MSFragger.

       MSGFPlusAdapter -- MS/MS database search using MS-GF+.

       MSSimulator -- A highly configurable simulator for mass spectrometry experiments.

       MSstatsConverter -- Converter to input for MSstats.

       MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate.

       MapAlignerIdentification  --  Corrects  retention  time  distortions between maps based on
       common peptide identifications.

       MapAlignerPoseClustering -- Corrects retention time distortions between maps using a  pose
       clustering approach.

       MapAlignerSpectrum  --  Corrects  retention  time  distortions  between  maps  by spectrum
       alignment.

       MapAlignerTreeGuided -- Tree guided correction of retention time distortions between maps.

       MapNormalizer -- Normalizes peak intensities in an MS run.

       MapRTTransformer -- Applies retention time transformations to maps.

       MapStatistics -- Extract extended statistics on the features of a map for quality control.

       MascotAdapter -- Annotates MS/MS spectra using Mascot.

       MascotAdapterOnline -- Annotates MS/MS spectra using Mascot.

       MassCalculator -- Calculates masses and mass-to-charge ratios of peptide sequences.

       MassTraceExtractor -- Detects mass traces in centroided LC-MS data.

       MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis.

       MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the
       same metabolite.

       MetaboliteSpectralMatcher -- Perform a spectral library search.

       MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them.

       MyriMatchAdapter -- Annotates MS/MS spectra using MyriMatch.

       MzMLSplitter -- Splits an mzML file into multiple parts.

       MzTabExporter -- Exports various XML formats to an mzTab file.

       NoiseFilterGaussian  --  Removes  noise  from profile spectra by using Gaussian filter (on
       uniform as well as non-uniform data).

       NoiseFilterSGolay -- Removes noise from profile spectra by using a Savitzky Golay  filter.
       Requires uniform (equidistant) data.

       NovorAdapter -- Template for Tool creation.

       NucleicAcidSearchEngine -- Annotate nucleic acid identifications to MS/MS spectra.

       OMSSAAdapter -- Annotates MS/MS spectra using OMSSA.

       OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers.

       OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers.

       OpenSwathAnalyzer -- Picks peaks and finds features in an SWATH-MS or SRM experiment.

       OpenSwathAssayGenerator  --  Generates assays according to different models for a specific
       TraML.

       OpenSwathChromatogramExtractor -- Extract chromatograms (XIC) from a MS2 map file.

       OpenSwathConfidenceScoring -- Compute confidence scores for OpenSwath results.

       OpenSwathDIAPreScoring -- Scoring spectra using the DIA scores.

       OpenSwathDecoyGenerator -- Generates decoys according to different models for  a  specific
       TraML.

       OpenSwathFeatureXMLToTSV -- Converts a featureXML to a mProphet tsv.

       OpenSwathFileSplitter -- Splits SWATH files into n files, each containing one window.

       OpenSwathMzMLFileCacher  --  This tool caches the spectra and chromatogram data of an mzML
       to disk.

       OpenSwathRTNormalizer -- 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.

       OpenSwathRewriteToFeatureXML -- Combines featureXML  and  mProphet  tsv  to  FDR  filtered
       featureXML.

       OpenSwathWorkflow -- Complete workflow to run OpenSWATH.

       PSMFeatureExtractor -- Computes extra features for each input PSM.

       PTModel -- Trains a model for the prediction of proteotypic peptides from a training set.

       PTPredict  -- predicts the likelihood of peptides to be proteotypic via svm_model which is
       trained by PTModel.

       PeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra.

       PeakPickerIterative -- Finds mass spectrometric peaks in profile mass spectra.

       PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra.

       PepNovoAdapter -- Adapter to PepNovo supporting all PepNovo command line  parameters.  The
       results are converted from the PepNovo text outfile format into the idXML format.

       PeptideIndexer -- Refreshes the protein references for all peptide hits.

       PercolatorAdapter -- Facilitate input to Percolator and reintegrate.

       PhosphoScoring  --  Scores  potential  phosphorylation sites in order to localize the most
       probable sites.

       PrecursorIonSelector -- PrecursorIonSelector.

       PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra,  by  using  MS1
       information.

       ProteinInference  --  Protein  inference  based  on  an  aggregation  of the scores of the
       identified peptides.

       ProteinQuantifier -- Compute peptide and protein abundances.

       ProteinResolver -- protein inference.

       ProteomicsLFQ -- A standard proteomics LFQ pipeline.

       QCCalculator -- Calculates basic quality parameters from  MS  experiments  and  subsequent
       analysis data as identification or feature detection.

       QCEmbedder -- Attaches a table or an image to a given qc parameter.

       QCExporter -- Will extract several qp from several run/sets in a tabular format.

       QCExtractor -- Extracts a table attachment to a given qc parameter.

       QCImporter -- Imports tables with quality control parameters into qcml files.

       QCMerger -- Merges two qcml files together.

       QCShrinker -- 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.

       QualityControl -- 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.

       RNADigestor -- Digests an RNA sequence database in-silico.

       RNAMassCalculator  --  Calculates  masses,  mass-to-charge  ratios and sum formulas of RNA
       sequences.

       RNPxlSearch -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra.

       RNPxlXICFilter -- Remove MS2 spectra from treatment  based  on  the  fold  change  between
       control and treatment.

       RTEvaluation  -- Application that evaluates TPs (true positives), TNs, FPs, and FNs for an
       idXML file with predicted RTs.

       RTModel -- Trains a model for the retention time prediction of peptides  from  a  training
       set.

       RTPredict -- Predicts retention times for peptides using a model trained by RTModel.

       Resampler -- Transforms an LC/MS map into a resampled map or a PNG image.

       SeedListGenerator -- Generates seed lists for feature detection.

       SemanticValidator -- SemanticValidator for semantically validating certain XML files.

       SequenceCoverageCalculator -- Prints information about idXML files.

       SimpleSearchEngine -- Annotates MS/MS spectra using SimpleSearchEngine.

       SiriusAdapter  --  Tool  for  metabolite  identification  using  single  and  tandem  mass
       spectrometry.

       SpecLibCreator -- Creates an MSP formatted spectral library.

       SpecLibSearcher -- Identifies peptide MS/MS spectra by spectral matching with a searchable
       spectral library.

       SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra.

       SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra.

       SpectraFilterNLargest -- Applies thresholdfilter to peak spectra.

       SpectraFilterNormalizer -- Normalizes intensity of peak spectra.

       SpectraFilterParentPeakMower -- Applies thresholdfilter to peak spectra.

       SpectraFilterScaler -- Applies thresholdfilter to peak spectra.

       SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra.

       SpectraFilterThresholdMower -- Applies thresholdfilter to peak spectra.

       SpectraFilterWindowMower -- Applies thresholdfilter to peak spectra.

       SpectraMerger -- Merges spectra (each MS level separately), increasing S/N ratios.

       SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable.

       StaticModification -- Applies a set of modifications to all PeptideIDs in an idXML file.

       SvmTheoreticalSpectrumGeneratorTrainer   --   Trainer   for   SVM   models  as  input  for
       SvmTheoreticalSpectrumGenerator.

       SwathWizard -- An assistant for Swath-Analysis.

       TICCalculator -- Calculates the TIC  from  a  mass  spectrometric  raw  file  (useful  for
       benchmarking).

       TOFCalibration -- Applies time of flight calibration.

       TOPPAS -- An assistant for GUI-driven TOPP workflow design.

       TOPPView -- A viewer for mass spectrometry data.

       TargetedFileConverter  --  Converts  different  transition files for targeted proteomics /
       metabolomics analysis.

       TextExporter -- Exports various XML formats to a text file.

       TransformationEvaluation -- Applies a transformation to a range of values.

       XFDR -- Calculates false discovery rate estimates on crosslink identifications.

       XMLValidator -- Validates XML files against an XSD schema.

       XTandemAdapter -- Annotates MS/MS spectra using X! Tandem.

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.    BMC
       Bioinformatics, 9:163. doi:10.1186/1471-2105-9-163.

SEE ALSO

       libopenms(3), openms-common(7), openms(7), openms-doc(7).

       The program is documented fully in the Tutorials, that are packaged in openms-doc.

AUTHOR

       This  manual  page  was  written  by  Filippo  Rusconi <lopippo@debian.org>. Permission is
       granted to copy, distribute and/or modify this document under the terms of the GNU General
       Public License, Version 3, published by the Free Software Foundation.

        On  a  Debian system the complete text of the GNU General Public License version 3 can be
       found in the file `/usr/share/common-licenses/GPL-3'.

                                          November 2012                                   TOPP(1)