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

• 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
• FLASHDeconvWizard - A user-friendly step-by-step wizard for the FLASHDeconv tool

File Converter

• FileConverter - Converts between different MS file formats.
• GNPSExport - Export MS/MS data in .MGF format for GNPS.
• IDFileConverter - Converts between different identification file formats.
• MSstatsConverter - Convert to MSstats input file format.
• MzTabExporter - Exports various XML formats to an mzTab file.
• TargetedFileConverter - Converts targeted files (such as tsv or TraML files).
• TextExporter - Exports various XML formats to a text file.
• TriqlerConverter - Convert to Triqler input file format.

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

• BaselineFilter - Removes the baseline from profile spectra using a top-hat filter.
• NoiseFilterGaussian - Removes noise from profile spectra using a Gaussian smoothing.
• NoiseFilterSGolay - Removes noise from profile spectra using Savitzky-Golay smoothing.
• MapNormalizer - Normalizes peak intensities in an MS run.
• SpectraFilterBernNorm - Scales and filters spectra according to the Bern norm.
• SpectraFilterNLargest - Keeps only the n largest peaks per spectrum.
• SpectraFilterNormalizer - Scale intensities per spectrum to either sum to 1 or have a maximum of 1.
• SpectraFilterScaler - Assigns new intensity per spectrum according to intensity rank.
• SpectraFilterSqrtMower - Scales the intensity of peaks to their sqrt.
• SpectraFilterThresholdMower - Removes all peaks below an intensity threshold.
• SpectraFilterWindowMower - Retains the highest peaks in a sliding or jumping window.

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

• InternalCalibration - Applies an internal mass calibration (using PSMs or fixed masses).
• ExternalCalibration - Applies an external mass calibration.
• HighResPrecursorMassCorrector - Correct the precursor entries of tandem MS scans for high resolution data.
• IDRTCalibration - Can be used to calibrate RTs of peptide hits linearly to standards.

Quantitation

• 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.
• 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.
• 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

• 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.

Targeted Experiments and OpenSWATH

• AssayGeneratorMetabo - Generates an assay library using DDA data (Metabolomics).
• AssayGeneratorMetaboSirius - Generates an assay library using SIRIUS project directory (Metabolomics).
• ClusterMassTracesByPrecursor - Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.
• MRMMapper - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
• MRMPairFinder - Evaluates labeled pair ratios on MRM features.
• MRMTransitionGroupPicker - Picks peaks in MRM chromatograms.
• 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.
• OpenSwathDIAPreScoring - SWATH (data-independent acquisition) pre-scoring.
• OpenSwathFeatureXMLToTSV - Converts a featureXML to a tsv.
• OpenSwathFileSplitter - Splitting a single SWATH / DIA file into a set of files, each containing one SWATH window.
• OpenSwathMzMLFileCacher - Caching of large mzML files.
• OpenSwathRewriteToFeatureXML - Rewrites results from mProphet back into featureXML.
• OpenSwathRTNormalizer - Align an SRM / SWATH run to a normalized retention time space.
• OpenSwathWorkflow - Complete workflow to run OpenSWATH.

Cross-linking

• 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

• AccurateMassSearch - Finds potential HMDB IDs within the given mass error window.
• MetaboliteSpectralMatcher - Identifies small molecules from tandem MS spectra.
• SiriusExport - Export for Sirius de novo metabolite identification.

RNA

• NucleicAcidSearchEngine - Search MzML files for oligonucleotides and their modifications.
• RNADigestor - Digests an RNA sequence database in-silico.
• RNAMassCalculator - Calculates masses and mass-to-charge ratios of RNA sequences.

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]

• CVInspector - Visualization and validation of PSI mapping and CV files.
• FuzzyDiff - Compares two files, tolerating numeric differences.
• JSONExporter - Exports .oms (SQLite) files in JSON format
• OpenMSDatabasesInfo - prints the content of OpenMS' enzyme and modification databases to a TSV file.
• SemanticValidator - SemanticValidator for analysisXML and mzML files.
• XMLValidator - Validates XML files against an XSD schema.