TOPP documentation

'TOPP - The OpenMS Proteomics Pipeline' is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem.

The TOPP tools are divided into several subgroups:

Graphical Tools

• TOPPView - A viewer for mass spectrometry data.
• TOPPAS - An assistant for GUI-driven TOPP workflow design.
• INIFileEditor - An editor for OpenMS configuration files.
• SwathWizard - A user-friendly step-by-step wizard for SWATH data analysis

File Handling

• DTAExtractor - Extracts spectra of an MS run file to several files in DTA format.
• 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.
• IDMerger - Merges several protein/peptide identification files into one file.
• IDRipper - Splits protein/peptide identifications according their file-origin.
• IDFileConverter - Converts identification engine file formats.
• MapStatistics - Extract extended statistics on the features of a map for quality control.
• TargetedFileConverter - Converts targeted files (such as tsv or TraML files).
• TextExporter - Exports various XML formats to a text file.
• MzTabExporter - Exports various XML formats to an mzTab file.

Signal Processing and Preprocessing

• BaselineFilter - Removes the baseline from profile spectra using a top-hat filter.
• InternalCalibration - Applies an internal mass calibration.
• ExternalCalibration - Applies an external mass calibration.
• MapNormalizer - Normalizes peak intensities in an MS run.
• MassTraceExtractor - Annotates mass traces in centroided LC-MS maps.
• NoiseFilterGaussian - Removes noise from profile spectra by using different smoothing techniques.
• NoiseFilterSGolay - Removes noise from profile spectra by using different smoothing techniques.
• PeakPickerHiRes - Finds mass spectrometric peaks in profile mass spectra.
• PeakPickerWavelet - Finds mass spectrometric peaks in profile mass spectra.
• PrecursorMassCorrector - Correct the precursor entries of tandem MS scans.
• HighResPrecursorMassCorrector - Correct the precursor entries of tandem MS scans for high resolution data.
• Resampler - Transforms an LC-MS map into an equally-spaced (in RT and m/z) map.
• SpectraFilterBernNorm - Applies a filter to peak spectra.
• SpectraFilterMarkerMower - Applies a filter to peak spectra.
• SpectraFilterNLargest - Applies a filter to peak spectra.
• SpectraFilterNormalizer - Applies a filter to peak spectra.
• SpectraFilterParentPeakMower - Applies a filter to peak spectra.
• SpectraFilterScaler - Applies a filter to peak spectra.
• SpectraFilterSqrtMower - Applies a filter to peak spectra.
• SpectraFilterThresholdMower - Applies a filter to peak spectra.
• SpectraFilterWindowMower - Applies a filter to peak spectra.
• SpectraMerger - Merges spectra from an LC-MS map, either by precursor or by RT blocks.
• TOFCalibration - Applies time of flight mass calibration.

Quantitation

• Decharger - Decharges and merges different feature charge variants of the same chemical entity.
• EICExtractor - Quantifies signals at given positions in (raw or picked) LC-MS maps.
• FeatureFinderCentroided - Detects two-dimensional features in centroided LC-MS data.
• FeatureFinderIdentification - Detects two-dimensional features in MS1 data based on peptide identifications.
• FeatureFinderIsotopeWavelet - Detects two-dimensional features in uncentroided (=raw) LC-MS data.
• FeatureFinderMetabo - Detects two-dimensional features in centroided LC-MS data of metabolites.
• FeatureFinderMRM - Quantifies features LC-MS/MS MRM data.
• FeatureFinderMultiplex - Identifies peptide multiplets (pairs, triplets etc., e.g. for SILAC or Dimethyl labeling) and determines their relative abundance.
• IsobaricAnalyzer - Extracts and normalizes TMT and iTRAQ information from an MS experiment.
• ProteinQuantifier - Computes protein abundances from annotated feature/consensus maps.
• ProteinResolver - A peptide-centric algorithm for protein inference.
• SeedListGenerator - Generates seed lists for feature detection.
• MetaProSIP - Detect labeled peptides from protein-SIP experiments.
• ProteomicsLFQ - Perform label-free quantification in a single tool.

Map Alignment

• ConsensusMapNormalizer - Normalizes maps of one consensusXML file (after linking).
• MapAlignerIdentification - Corrects RT distortions between maps based on common peptide identifications using one map as reference.
• MapAlignerTreeGuided - Corrects RT distortions between maps based on common peptide identifications guided by a similarity tree.
• MapAlignerPoseClustering - Corrects RT distortions between maps using a pose clustering approach (not using pep-ids and a linear model).
• MapAlignerSpectrum - Corrects RT distortions between maps by spectrum alignment.
• MapRTTransformer - Applies RT transformations to maps.
• FeatureLinkerLabeled - Groups corresponding isotope-labeled features in a feature map.
• FeatureLinkerUnlabeled - Groups corresponding features from multiple maps.
• FeatureLinkerUnlabeledQT - Groups corresponding features from multiple maps using a QT clustering approach.
• FeatureLinkerUnlabeledKD - Groups corresponding features from multiple maps using a KD tree.

Protein/Peptide Identification

• CometAdapter - Identifies MS/MS spectra using Comet (external).
• CompNovo - Performs a peptide/protein identification with the CompNovo engine.
• CompNovoCID - Performs a peptide/protein identification with the CompNovo engine in CID mode.
• CruxAdapter - Identifies peptides in MS/MS spectra via Crux and tide-search (external).
• MascotAdapter - Identifies MS/MS spectra using Mascot (external).
• MascotAdapterOnline - Identifies MS/MS spectra using Mascot (external).
• MSGFPlusAdapter - Identifies MS/MS spectra using MSGFPlus (external).
• MyriMatchAdapter - Identifies MS/MS spectra using MyriMatch (external).
• OMSSAAdapter - Identifies MS/MS spectra using OMSSA (external).
• PepNovoAdapter - Identifies MS/MS spectra using PepNovo (external).
• SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
• SimpleSearchEngine - A simple database search engine for annotating MS/MS spectra.
• XTandemAdapter - Identifies MS/MS spectra using XTandem (external).

Protein/Peptide Processing

• ConsensusID - Computes a consensus identification from peptide identifications of several identification engines.
• FalseDiscoveryRate - Estimates the false discovery rate on peptide and protein level using decoy searches.
• FidoAdapter - Runs the protein inference engine Fido.
• IDConflictResolver - Resolves ambiguous annotations of features with peptide identifications.
• IDFilter - Filters results from protein or peptide identification engines based on different criteria.
• IDMapper - Assigns protein/peptide identifications to feature or consensus features.
• IDPosteriorErrorProbability - Estimates posterior error probabilities using a mixture model.
• IDRTCalibration - Can be used to calibrate RTs of peptide hits linearly to standards.
• LuciphorAdapter - Scores potential phosphorylation sites in order to localize the most probable sites.
• PeptideIndexer - Refreshes the protein references for all peptide hits.
• PhosphoScoring - Scores potential phosphorylation sites in order to localize the most probable sites.
• ProteinInference - Infer proteins from a list of (high-confidence) peptides.
• PercolatorAdapter - Applies the percolator algorithm to protein/peptide identifications.

Targeted Experiments and OpenSWATH

• OpenSwathWorkflow - Complete workflow to run OpenSWATH.
• AssayGeneratorMetabo - Generates an assay library using DDA data (Metabolomics).
• InclusionExclusionListCreator - Creates inclusion and/or exclusion lists for LC-MS/MS experiments.
• MRMMapper - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
• MRMTransitionGroupPicker - Picks peaks in MRM chromatograms.
• PrecursorIonSelector - A tool for precursor ion selection based on identification results.
• OpenSwathAnalyzer - Picks peaks and finds features in an SRM experiment.
• OpenSwathAssayGenerator - Generates filtered and optimized assays using TraML files.
• OpenSwathChromatogramExtractor - Extract chromatograms (XIC) from a MS2 map file.
• OpenSwathConfidenceScoring - Computes confidence scores for OpenSwath results.
• OpenSwathDecoyGenerator - Generates decoys according to different models for a specific TraML.
• OpenSwathFeatureXMLToTSV - Converts a featureXML to a tsv.
• OpenSwathRTNormalizer - This tool will align an SRM / SWATH run to a normalized retention time space.

Peptide Property Prediction

• PTModel - Trains a model for the prediction of proteotypic peptides from a training set.
• PTPredict - Predicts the likelihood of peptides to be proteotypic using a model trained by PTModel.
• 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.

Cross-linking

• OpenPepXL - Search for peptide pairs linked with a labeled cross-linker.
• OpenPepXLLF - Search for cross-linked peptide pairs in tandem MS spectra.
• XFDR - Calculates false discovery rate estimates on cross-link identifications.

Quality Control

• QualityControl - A one-in-all QC tool to generate an augmented mzTab
• DatabaseSuitability - Calculates the suitability of a database for peptide identification search using a de novo approach.

Misc

• GenericWrapper - Allows the generic wrapping of external tools.
• ExecutePipeline - Executes workflows created by TOPPAS.
• GNPSExport - Export MS/MS data in .MGF format for GNPS.
• MaRaClusterAdapter - Run the spectral clustering implemented in MaRaCluster.