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

File Handling

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

File Converter

• FileConverter - Converts between different MS file formats.
• IDFileConverter - Converts between different identification file formats.
• TargetedFileConverter - Converts targeted files (such as tsv or TraML files).
• MSstatsConverter - Convert to MSstats input file format.
• TriqlerConverter - Convert to Triqler input file format.

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

• PeakPickerHiRes - Finds mass spectrometric peaks in profile mass spectra.
• PeakPickerWavelet - Finds mass spectrometric peaks in profile mass spectra.

Spectrum processing: peak filtering

• 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.
• BaselineFilter - Removes the baseline from profile spectra using a top-hat filter.
• NoiseFilterGaussian - Removes noise from profile spectra by using different smoothing techniques.
• NoiseFilterSGolay - Removes noise from profile spectra by using different smoothing techniques. Spectrum processing: peak normalization
• MapNormalizer - Normalizes peak intensities in an MS run.

Mass Correction and Calibration

• InternalCalibration - Applies an internal mass calibration.
• ExternalCalibration - Applies an external mass calibration.
• HighResPrecursorMassCorrector - Correct the precursor entries of tandem MS scans for high resolution data.
• PrecursorMassCorrector - Correct the precursor entries of tandem MS scans (low-res only).
• TOFCalibration - Applies time of flight mass 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

• MaRaClusterAdapter - Run the spectral clustering implemented in MaRaCluster.

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

• 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.

Quantitation

• ConsensusMapNormalizer - Normalizes maps of one consensusXML file (after linking).
• MassTraceExtractor - Annotates mass traces in centroided LC-MS maps.
• 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 (low-res).
• 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.
• MetaProSIP - Detect labeled peptides from protein-SIP experiments.
• ProteomicsLFQ - Perform label-free quantification in a single tool.

Protein/Peptide Identification

• CometAdapter - Identifies MS/MS spectra using Comet (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).
• TOPP_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.
• 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).
• MRMMapper - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
• 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.
• OpenSwathFeatureXMLToTSV - Converts a featureXML to a tsv.
• OpenSwathRTNormalizer - This tool will align an SRM / SWATH run to a normalized retention time space.

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

• GenericWrapper - Allows the generic wrapping of external tools.
• ExecutePipeline - Executes workflows created by TOPPAS.
• GNPSExport - Export MS/MS data in .MGF format for GNPS.

Top down

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

Besides TOPP, OpenMS offers a range of other tools categorized as utilities. They are not part of typical analysis pipelines, but they still might be very helpful to you. The tools categorized as utilities are divided into several subgroups:

Maintenance

• INIUpdater - Updates INI and TOPPAS files from previous versions of OpenMS as parameters and storage method might have change

Signal Processing and Preprocessing

• PeakPickerIterative - A tool for peak detection in profile data.

File Handling

• FuzzyDiff - Compares two files, tolerating numeric differences.
• IDSplitter - Splits protein/peptide identifications off of annotated data files.
• MzMLSplitter - Splits an mzML file into multiple parts.
• SemanticValidator - SemanticValidator for analysisXML and mzML files.
• XMLValidator - Validates XML files against an XSD schema.

Protein/Peptide Identification

• DatabaseFilter - Filters a protein database in FASTA format according to one or multiple filtering criteria.
• DecoyDatabase - Creates decoy peptide databases from normal ones.
• 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.
• IDExtractor - Extracts n peptides randomly or best n from idXML files.
• IDMassAccuracy - Calculates a distribution of the mass error from given mass spectra and IDs.
• IDScoreSwitcher - Switches between different scores of peptide or protein hits in identification data.
• MSFraggerAdapter - Peptide Identification with MSFragger.
• NovorAdapter - De novo sequencing from tandem mass spectrometry data.
• PSMFeatureExtractor - Creates search engine specific features for PercolatorAdapter input.
• SequenceCoverageCalculator - Prints information about idXML files.
• SpecLibCreator - Creates an MSP-formatted spectral library.
• SpectraSTSearchAdapter - An interface to the 'SEARCH' mode of the SpectraST program (external, beta).
• 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.

Cross-linking

• RNPxlSearch - Annotates RNA-to-peptide cross-links in MS/MS spectra.
• RNPxlXICFilter - Removes MS2 spectra from treatment based on the fold change between control and treatment for RNA-to-peptide cross-linking experiments.

Quantitation

• ERPairFinder - Evaluates pair ratios on enhanced resolution (zoom) scans.
• FeatureFinderMetaboIdent - Detects features in MS1 data corresponding to small molecule identifications.
• ProteomicsLFQ - A standard Proteomics LFQ pipeline.
• MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule.
• MultiplexResolver - Resolves conflicts between identifications and quantifications in multiplex data.

Metabolite Identification

• AccurateMassSearch - Finds potential HMDB IDs within the given mass error window.
• MetaboliteSpectralMatcher - Identifies small molecules from tandem MS spectra.
• SiriusAdapter - De novo metabolite identification.

Targeted Experiments and OpenSWATH

• ClusterMassTracesByPrecursor - Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.
• MRMPairFinder - Evaluates labeled pair ratios on MRM features.
• OpenSwathDIAPreScoring - SWATH (data-independent acquisition) pre-scoring.
• OpenSwathFileSplitter - A tool for 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.

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.

Quality Control

• 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.

Misc

• ClusterMassTraces - Cluster mass traces occurring in the same map together.
• DeMeanderize - Orders the spectra of MALDI spotting plates correctly.
• ImageCreator - Creates images from MS1 data (with MS2 data points indicated as dots).
• MassCalculator - Calculates masses and mass-to-charge ratios of peptide sequences.
• MetaProSIP - Performs proteinSIP on peptide features for elemental flux analysis.
• TICCalculator - Calculates the TIC of a raw mass spectrometric file.
• MSstatsConverter - Converter to input for MSstats.

Deprecated

• IDDecoyProbability - Estimates peptide probabilities using a decoy search strategy. WARNING: This utility is deprecated.