OpenMS  3.0.0
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:

File Handling

  • DTAExtractor - Extracts spectra of an MS run file to several files in DTA format.

File Converter

File Handling

  • FileFilter - Extracts or manipulates portions of data from peak, feature or consensus feature files.
  • DatabaseFilter - Filter protein databases.
  • 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.
  • TextExporter - Exports various XML formats to a text file.
  • MzTabExporter - Exports various XML formats to an mzTab file.
  • DTAExtractor - Extracts spectra of an MS run file to several files in DTA format.
  • 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.

Centroiding

Spectrum processing: peak filtering

Mass Correction and Calibration

Spectrum processing: Misc

  • Resampler - Transforms an LC-MS map into an equally-spaced (in RT and m/z) map.
  • SpectraMerger - Merges spectra from an LC-MS map, either by precursor or by RT blocks.

Spectrum Clustering

Map Alignment

  • 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.

Feature linking

Quantitation

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

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