| OpenMS 2.5.0

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.

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.

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).
- InspectAdapter - Identifies MS/MS spectra using Inspect (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.

Misc

- QualityControl - A one-in-all QC tool to generate an augmented mzTab
- 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.