TOPP

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 â 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’.