'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:
- TOPPView - A viewer for mass spectrometry data.
- TOPPAS - An assistant for GUI-driven TOPP workflow design.
- INIFileEditor - An editor for OpenMS configuration files.
- 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.
- TextExporter - Exports various XML formats to a text file.
- MzTabExporter - Exports various XML formats to an mzTab file
Signal Processing and Preprocessing
- AdditiveSeries - Computes an additive series to quantify a peptide in a set of samples.
- 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.
- CompNovo - Performs a peptide/protein identification with the CompNovo engine.
- CompNovoCID - Performs a peptide/protein identification with the CompNovo engine in CID mode.
- 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).
- XTandemAdapter - Identifies MS/MS spectra using XTandem (external).
- SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
- 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.
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.