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


       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.


       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

       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

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

       FeatureLinkerUnlabeled  --  Groups corresponding features from multiple

       FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple

       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

       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

       InspectAdapter -- Annotates MS/MS spectra using Inspect.

       InternalCalibration -- Applies an internal calibration.

       IsobaricAnalyzer  --  Calculates  isobaric  quantitative   values   for

       LabeledEval   --   Evaluation  tool  for  isotope-labeled  quantitation

       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

       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

       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

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

       OpenSwathConfidenceScoring  --  Compute confidence scores for OpenSwath

       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

       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

       PeakPickerWavelet  --  Finds  mass  spectrometric peaks in profile mass

       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

       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

       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

       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

       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

       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

       XMLValidator -- Validates XML files against an XSD schema.

       XTandemAdapter -- Annotates MS/MS spectra using XTandem.


       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.


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

       The  program is documented fully in the Tutorials, that are packaged in


       This manual page was written by Filippo  Rusconi  <>.
       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)

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