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)