TOPP documentation

'TOPP - The OpenMS 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

File Converter

File Filtering / Extraction / Merging

  • DatabaseFilter - Filter protein databases.
  • DecoyDatabase - Creates decoy peptide databases from normal ones.
  • DTAExtractor - Extracts spectra of an MS run file to several files in DTA format.
  • 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.
  • IDFilter - Filters results from protein or peptide identification engines based on different criteria.
  • IDMerger - Merges several protein/peptide identification files into one file.
  • IDRipper - Splits protein/peptide identifications according their file-origin.
  • IDSplitter - Splits protein/peptide identifications off of annotated data files.
  • IonMobilityBinning - Merges spectra with similar IM values and creates N output mzML's by discretizing the IM range.
  • MapStatistics - Extract extended statistics on the features of a map for quality control.
  • MzMLSplitter - Splits an mzML file into multiple parts.

Spectrum processing: Centroiding

  • PeakPickerHiRes - Peak detection in high-resolution profile mass spectra.
  • PeakPickerIterative - Peak detection in high-resolution profile TOF data (based on PeakPickerHiRes with some postprocessing)

Spectrum processing: peak smoothing / normalization

Spectrum processing: Misc / Helpers

  • MaRaClusterAdapter - Run the spectral clustering implemented in MaRaCluster.
  • 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.

Mass Correction and Calibration


  • ConsensusMapNormalizer - Normalizes maps of one consensusXML file (after linking).
  • 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.
  • FeatureFinderMetabo - Detects two-dimensional features in centroided LC-MS data of metabolites.
  • FeatureFinderMetaboIdent - Detects features in MS1 data corresponding to small molecule identifications.
  • 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.
  • MassTraceExtractor - Annotates mass traces in centroided LC-MS maps.
  • MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule.
  • MetaProSIP - Detect labeled peptides from protein-SIP experiments.
  • MultiplexResolver - Resolves conflicts between identifications and quantifications in multiplex data.
  • ProteinQuantifier - Computes protein abundances from annotated feature/consensus maps.
  • ProteomicsLFQ - Perform label-free quantification in a single tool.
  • SeedListGenerator - Generates seed lists for feature detection.

Identification of Proteins/Peptides (SearchEngines)

  • CometAdapter - Identifies MS/MS spectra using Comet (external).
  • LuciphorAdapter - Scores potential phosphorylation sites in order to localize the most probable sites.
  • MascotAdapter - Identifies MS/MS spectra using Mascot (external).
  • MascotAdapterOnline - Identifies MS/MS spectra using Mascot (external).
  • MSFraggerAdapter - Peptide Identification with MSFragger.
  • MSGFPlusAdapter - Identifies MS/MS spectra using MSGFPlus (external).
  • NovorAdapter - De novo sequencing from tandem mass spectrometry data.
  • SageAdapter - Identifies MS/MS spectra using Sage (external).
  • SimpleSearchEngine - A simple database search engine for annotating MS/MS spectra.
  • SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
  • SpectraSTSearchAdapter - An interface to the 'SEARCH' mode of the SpectraST program (external, beta).
  • XTandemAdapter - Identifies MS/MS spectra using XTandem (external).

Identification Processing

  • ConsensusID - Computes a consensus identification from peptide identifications of several identification engines.
  • Digestor - Digests a protein database in-silico.
  • DigestorMotif - Digests a protein database in-silico (optionally allowing only peptides with a specific motif) and produces statistical data for all peptides.
  • Epifany - Bayesian protein inference based on PSM probabilities.
  • FalseDiscoveryRate - Estimates the false discovery rate on peptide and protein level using decoy searches.
  • IDConflictResolver - Resolves ambiguous annotations of features with peptide identifications.
  • IDDecoyProbability - Estimates peptide probabilities using a decoy search strategy. WARNING: This utility is deprecated.
  • IDExtractor - Extracts n peptides randomly or best n from idXML files.
  • IDMapper - Assigns protein/peptide identifications to feature or consensus features.
  • IDMassAccuracy - Calculates a distribution of the mass error from given mass spectra and IDs.
  • IDPosteriorErrorProbability - Estimates posterior error probabilities using a mixture model.
  • IDScoreSwitcher - Switches between different scores of peptide or protein hits in identification data.
  • PeptideIndexer - Refreshes the protein references for all peptide hits.
  • PercolatorAdapter - Applies the percolator algorithm to protein/peptide identifications.
  • PhosphoScoring - Scores potential phosphorylation sites in order to localize the most probable sites.
  • ProteinInference - Infer proteins from a list of (high-confidence) peptides.
  • PSMFeatureExtractor - Creates search engine specific features for PercolatorAdapter input.
  • SequenceCoverageCalculator - Prints information about idXML files.
  • SpecLibCreator - Creates an MSP-formatted spectral library.
  • StaticModification - Allows to attach a set of fixed modifications to an idXML file (MS/MS search results), e.g. to add 15N (N15) labeling post-hoc.

Map Alignment

  • MapAlignerIdentification - Corrects RT distortions between maps based on common peptide identifications using one map as reference.
  • MapAlignerPoseClustering - Corrects RT distortions between maps using a pose clustering approach (not using pep-ids and a linear model).
  • MapAlignerTreeGuided - Corrects RT distortions between maps based on common peptide identifications guided by a similarity tree.
  • MapRTTransformer - Applies RT transformations to maps.

Feature linking

Targeted Experiments and OpenSWATH


  • OpenPepXL - Search for peptide pairs linked with a labeled cross-linker.
  • OpenPepXLLF - Search for cross-linked peptide pairs in tandem MS spectra.
  • RNPxlXICFilter - Removes MS2 spectra from treatment based on the fold change between control and treatment for RNA-to-peptide cross-linking experiments.
  • XFDR - Calculates false discovery rate estimates on cross-link identifications.

Top down

  • FLASHDeconv - Computes a feature deconvolution from Top down MS data.

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.
  • QCCalculator - Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file.
  • QCEmbedder - Embeds tables or plots generated externally as attachments to existing quality parameters in qcML files.
  • QCExporter - Extracts several quality parameter from several runs/sets from a qcML file into a tabular (text) format - counterpart to QCImporter.
  • QCExtractor - Extracts a table attachment of a given quality parameter from a qcML file as tabular (text) format.
  • QCImporter - Imports several quality parameters from a tabular (text) format into a qcML file - counterpart to QCExporter.
  • QCMerger - Merges two qcML files together.
  • QCShrinker - Removes extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report.

Metabolite Identification


Misc / Helpers

  • ClusterMassTraces - Cluster mass traces occurring in the same map together.
  • DeMeanderize - Orders the spectra of MALDI spotting plates correctly.
  • ExecutePipeline - Executes workflows created by TOPPAS.
  • GenericWrapper - Allows the generic wrapping of external tools.
  • ImageCreator - Creates images from MS1 data (with MS2 data points indicated as dots).
  • INIUpdater - Updates INI and TOPPAS files from previous versions of OpenMS as parameters and storage method might have change
  • MassCalculator - Calculates masses and mass-to-charge ratios of peptide sequences.
  • MetaProSIP - Performs proteinSIP on peptide features for elemental flux analysis.
  • OpenMSInfo - Print system information.
  • TICCalculator - Calculates the TIC of a raw mass spectrometric file.

[for developers]