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 -- Find potential HMDB ids within the given mass error window.

       AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples.

       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.

       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 identification from peptide identifications of several
       identification engines.

       ConsensusMapNormalizer -- Normalizes maps of one consensusXML file.

       ConvertTSVToTraML -- Converts an OpenSWATH transition TSV file to a TraML file.

       ConvertTraMLToTSV -- Converts a TraML file to an OpenSWATH transition TSV file.

       DBExporter -- Exports data from an OpenMS database to a file.

       DBImporter -- Imports data to an OpenMS database.

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

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

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

       DecoyDatabase -- Create decoy peptide databases from normal ones.

       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.

       ExecutePipeline -- Executes workflows created by TOPPAS.

       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.

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

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

       FeatureFinderMetabo -- Assembles metabolite features from singleton mass traces.

       FeatureFinderRaw -- 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.

       FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple maps.

       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.

       GenericWrapper -- Allows the generic wrapping of external tools.

       HighResPrecursorMassCorrector -- Corrects the precursor mz determined  by  the  instrument
       software.

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

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

       IDEvaluatorGUI  --  Computes  a  'q-value  vs.  #PSM'  plot  to   visualize   the   number
       identifications for a certain q-value.

       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
       annotated file origin.

       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.

       ITRAQAnalyzer -- Calculates iTRAQ quantitative values for peptides.

       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 calibration.

       IsobaricAnalyzer -- Calculates isobaric quantitative values for peptides.

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

       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.

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

       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.

       MapAlignmentEvaluation -- Evaluates alignment results against a ground truth.

       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.

       MyriMatchAdapter -- Annotates MS/MS spectra using MyriMatch.

       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.

       OMSSAAdapter -- Annotates MS/MS spectra using OMSSA.

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

       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.

       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 transoform  the  RT
       space into the normalized space.

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

       PILISIdentification -- performs a peptide/protein identification with the PILIS engine.

       PILISModelCV -- Perform a cross validation of the PILIS model parameters.

       PILISModelTrainer  --  Train  the  PILIS  model  with  a  given   set   of   spectra   and
       identifications.

       PILISSpectraGenerator -- Generate spectra given a list of peptides and a PILIS model.

       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.

       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.

       PhosphoScoring  -- Scores potential phosphorylation sites and therby tries 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 the number of identified peptides.

       ProteinQuantifier -- Compute peptide and protein abundances.

       ProteinResolver -- protein inference.

       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.

       RNPxl -- Tool for RNP cross linking experiment analysis.

       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.

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

       SeedListGenerator -- Generates seed lists for feature detection.

       SemanticValidator -- SemanticValidator for analysisXML and mzML files.

       SequenceCoverageCalculator -- Prints information about idXML files.

       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 -- Applies thresholdfilter to 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.

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

       TMTAnalyzer -- Calculates TMT quantitative values for peptides.

       TOFCalibration -- Applies time of flight calibration.

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

       TOPPView -- A viewer for mass spectrometry data.

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

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

       XMLValidator -- Validates XML files against an XSD schema.

       XTandemAdapter -- Annotates MS/MS spectra using XTandem.

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)