| OpenMS Developer Quickstart Guide | |
| ChangeLog | |
| FAQ | |
| Known Issues | |
| Developer C++ Quickstart Guide | |
| pyOpenMS (Python bindings) | |
| ▼User Quickstart Guide | |
| ►TOPP tutorial | |
| TOPP and OpenMS | |
| Introduction | |
| The views | |
| Display modes and view options | |
| Data analysis | |
| Data editing | |
| Hotkeys table | |
| Smoothing raw data | |
| Subtracting a baseline from a spectrum | |
| Picking peaks | |
| Feature detection on centroided data | |
| TOPP for Advanced Users | |
| ►General introduction | |
| INIFileEditor | Can be used to visually edit INI files of TOPP tools |
| INIUpdater | Update INI and TOPPAS files from previous versions of OpenMS/TOPP |
| File Handling | |
| Profile data processing | |
| Calibration | |
| Map alignment | |
| Feature detection | |
| Feature grouping | |
| Consensus peptide identification | |
| Peptide property prediction | |
| Quality Control | |
| Conversion between OpenMS XML formats and text formats | |
| ►TOPP documentation | |
| TOPPView | |
| TOPPAS | An assistant for GUI-driven TOPP workflow design |
| INIFileEditor | Can be used to visually edit INI files of TOPP tools |
| DTAExtractor | Extracts scans of an mzML file to several files in DTA format |
| FileConverter | Converts between different MS file formats |
| FileFilter | Extracts portions of the data from an mzML, featureXML or consensusXML file |
| FileInfo | Shows basic information about the data in an OpenMS readable file |
| FileMerger | Merges several files. Multiple output format supported, depending on input format |
| IDMerger | Merges several idXML files into one idXML file |
| IDRipper | IDRipper splits the protein/peptide identifications of an idXML file into several idXML files according their annotated file origin |
| IDFileConverter | Converts peptide/protein identification engine file formats |
| MapStatistics | Extract extended statistics on the features of a map for quality control |
| TargetedFileConverter | Converts different spectral libraries / transition files for targeted proteomics and metabolomics analysis |
| TextExporter | This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to text files |
| MzTabExporter | This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to mzTab |
| BaselineFilter | Executes the top-hat filter to remove the baseline of an MS experiment |
| InternalCalibration | Performs an internal mass recalibration on an MS experiment |
| ExternalCalibration | Performs an mass recalibration on an MS experiment using an external calibration function |
| MapNormalizer | Normalizes peak intensities to the percentage of the maximum intensity in the HPLC-MS map |
| MassTraceExtractor | MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile |
| NoiseFilterGaussian | Executes a Gaussian filter to reduce the noise in an MS experiment |
| NoiseFilterSGolay | Executes a Savitzky Golay filter to reduce the noise in an MS experiment |
| PeakPickerHiRes | A tool for peak detection in profile data. Executes the peak picking with high_res algorithm |
| PeakPickerWavelet | A tool for peak detection in profile data. Executes the peak picking with the algorithm described in described in Lange et al. (2006) Proc. PSB-06 |
| PrecursorMassCorrector | Corrects the precursor entries of MS/MS spectra, by using MS1 information |
| HighResPrecursorMassCorrector | Corrects the precursor mz of high resolution data |
| Resampler | Resampler can be used to transform an LC/MS map into a resampled map |
| SpectraFilterBernNorm | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterMarkerMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterNLargest | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterNormalizer | Normalizes intensity of peak spectra |
| SpectraFilterParentPeakMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterScaler | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterSqrtMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterThresholdMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterWindowMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraMerger | Allows to add up several spectra |
| TOFCalibration | Performs an external calibration for tof spectra |
| Decharger | Decharges a feature map by clustering charge variants of a peptide to zero-charge entities |
| EICExtractor | Extracts EICs from an MS experiment, in order to quantify analytes at a given position |
| FeatureFinderCentroided | The feature detection application for quantitation (centroided) |
| FeatureFinderIdentification | Detects features in MS1 data based on peptide identifications |
| FeatureFinderIsotopeWavelet | The feature detection application for quantitation |
| FeatureFinderMetabo | FeatureFinderMetabo assembles metabolite features from singleton mass traces |
| FeatureFinderMRM | The feature detection application for quantitation |
| FeatureFinderMultiplex | Detects peptide pairs in LC-MS data and determines their relative abundance |
| IsobaricAnalyzer | Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment |
| ProteinQuantifier | Compute peptide and protein abundances from annotated feature/consensus maps or from identification results |
| ProteinResolver | A peptide-centric algorithm for protein inference |
| SeedListGenerator | Application to generate seed lists for feature detection |
| MetaProSIP | Performs proteinSIP on peptide features for elemental flux analysis |
| ProteomicsLFQ | |
| ConsensusMapNormalizer | Normalization of intensities in a set of maps using robust regression |
| MapAlignerIdentification | Corrects retention time distortions between maps, using information from peptides identified in different maps |
| MapAlignerTreeGuided | Corrects retention time distortions between maps, using information from peptides identified in different maps |
| MapAlignerPoseClustering | Corrects retention time distortions between maps, using a pose clustering approach |
| MapAlignerSpectrum | Corrects retention time distortions between maps by aligning spectra |
| MapRTTransformer | Applies retention time transformations to maps |
| FeatureLinkerLabeled | Groups corresponding isotope-labeled features in a feature map |
| ►FeatureLinkerUnlabeled | Groups corresponding features from multiple maps |
| FileConverter | Converts between different MS file formats |
| FeatureLinkerUnlabeledQT | Groups corresponding features from multiple maps using a QT clustering approach |
| FeatureLinkerUnlabeledKD | Group corresponding features across labelfree experiments |
| CometAdapter | Identifies peptides in MS/MS spectra via Comet |
| CompNovo | Performs a peptide/protein identification with the CompNovo engine |
| CompNovoCID | Performs a peptide/protein identification with the CompNovo engine |
| CruxAdapter | Identifies peptides in MS/MS spectra via Crux and tide-search |
| InspectAdapter | Identifies peptides in MS/MS spectra via Inspect |
| MascotAdapter | Identifies peptides in MS/MS spectra via Mascot |
| MascotAdapterOnline | Identifies peptides in MS/MS spectra via Mascot |
| ►MSGFPlusAdapter | Adapter for the MS-GF+ protein identification (database search) engine |
| TOPP for Advanced Users | |
| MyriMatchAdapter | Identifies peptides in MS/MS spectra via MyriMatch |
| ►OMSSAAdapter | Identifies peptides in MS/MS spectra via OMSSA (Open Mass Spectrometry Search Algorithm) |
| TOPP for Advanced Users | |
| PepNovoAdapter | Identifies peptides in MS/MS spectra via PepNovo |
| SpecLibSearcher | Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library |
| SimpleSearchEngine | Identifies peptides in MS/MS spectra |
| ►XTandemAdapter | Identifies peptides in MS/MS spectra via the search engine X! Tandem |
| TOPP for Advanced Users | |
| ConsensusID | Computes a consensus from results of multiple peptide identification engines |
| FalseDiscoveryRate | Tool to estimate the false discovery rate on peptide and protein level |
| FidoAdapter | Runs the protein inference engine Fido |
| IDConflictResolver | Resolves ambiguous annotations of features with peptide identifications |
| IDFilter | Filters peptide/protein identification results by different criteria |
| IDMapper | Assigns protein/peptide identifications to features or consensus features |
| IDPosteriorErrorProbability | Tool to estimate the probability of peptide hits to be incorrectly assigned |
| IDRTCalibration | Can be used to calibrate the RTs of peptide hits linearly to standards |
| LuciphorAdapter | Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data |
| ►PeptideIndexer | Refreshes the protein references for all peptide hits from an idXML file and adds target/decoy information |
| TOPP for Advanced Users | |
| PhosphoScoring | Tool to score phosphorylation sites of peptides |
| ProteinInference | Computes a protein identification score based on an aggregation of scores of identified peptides |
| PercolatorAdapter | PercolatorAdapter facilitates the input to, the call of and output integration of Percolator. Percolator (http://per-colator.com/) is a tool to apply semi-supervised learning for peptide identification from shotgun proteomics datasets |
| OpenSwathWorkflow | Complete workflow to run OpenSWATH |
| AssayGeneratorMetabo | Generates an assay library using DDA data (Metabolomics) |
| InclusionExclusionListCreator | A tool for creating inclusion and/or exclusion lists for LC-MS/MS |
| MRMMapper | MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) |
| MRMTransitionGroupPicker | Picks peaks in SRM/MRM chromatograms that belong to the same precursors |
| PrecursorIonSelector | A tool for precursor ion selection based on identification results |
| OpenSwathAnalyzer | Executes a peak-picking and scoring algorithm on MRM/SRM data |
| OpenSwathAssayGenerator | Generates filtered and optimized assays using TraML files |
| OpenSwathChromatogramExtractor | Extracts chromatograms (XICs) from a file containing spectra |
| OpenSwathConfidenceScoring | Computes confidence scores for OpenSwath results |
| OpenSwathDecoyGenerator | Generates decoys according to different models for a specific TraML |
| OpenSwathFeatureXMLToTSV | Converts a featureXML to a mProphet tsv |
| OpenSwathRTNormalizer | The OpenSwathRTNormalizer will find retention time peptides in data |
| PTModel | Used to train a model for the prediction of proteotypic peptides |
| PTPredict | This application is used to predict the likelihood of peptides to be proteotypic |
| RTModel | Used to train a model for peptide retention time prediction or peptide separation prediction |
| RTPredict | This application is used to predict retention times for peptides or peptide separation |
| QualityControl | Generates an mzTab file from various sources of a pipeline (mainly a ConsensusXML) which can be used for QC plots (e.g. via the R package 'PTX-QC') |
| GenericWrapper | Allows generically the wrapping of external tools |
| ExecutePipeline | Executes workflows created by TOPPAS |
| GNPSExport | Export MS/MS data in .MGF format for GNPS (http://gnps.ucsd.edu) |
| MaRaClusterAdapter | MaRaClusterAdapter facilitates the input to, the call of and output integration of MaRaCluster. MaRaCluster (https://github.com/statisticalbiotechnology/maracluster) is a tool to apply unsupervised clustering of ms2 spectra from shotgun proteomics datasets |
| ►UTILS documentation | |
| INIUpdater | Update INI and TOPPAS files from previous versions of OpenMS/TOPP |
| LowMemPeakPickerHiRes | A tool for peak detection on streamed profile data (low-memory requirements). Executes the peak picking with high_res algorithm |
| LowMemPeakPickerHiResRandomAccess | A tool for peak detection in profile data. Executes the peak picking with high_res algorithm |
| PeakPickerIterative | A tool for peak detection in profile data. Executes the peak picking with high_res algorithm |
| CVInspector | A tool for visualization and validation of PSI mapping and CV files |
| 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 XML files which can be semantically validated |
| XMLValidator | Validates XML files against an XSD schema |
| FFEval | Evaluation tool for feature detection algorithms |
| LabeledEval | Evaluation tool for isotope-labeled quantitation experiments |
| RTEvaluation | Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs |
| TransformationEvaluation | Applies a transformation to a range of values and records the results |
| DatabaseFilter | The DatabaseFilter tool filters a protein database in fasta format according to one or multiple filtering criteria |
| DecoyDatabase | Create a decoy peptide database from standard FASTA databases |
| Digestor | Digests a protein database in-silico |
| DigestorMotif | This application is used to digest a protein database to get all peptides given a cleavage enzyme. It will also produce peptide statistics given the mass accuracy of the instrument. You can extract peptides with specific motifs,e.g. onyl cysteine containing peptides for ICAT experiments. At the moment only trypsin is supported |
| Epifany | EPIFANY - Efficient protein inference for any peptide-protein network is a Bayesian protein inference engine. It uses PSM (posterior) probabilities from Percolator, OpenMS' IDPosteriorErrorProbability or similar tools to calculate posterior probabilities for proteins and protein groups |
| 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 hits (PSMs) or protein hits in identification data |
| MSFraggerAdapter | Peptide Identification with MSFragger |
| NovorAdapter | Novoradapter for de novo sequencing from tandem mass spectrometry data |
| PSMFeatureExtractor | PSMFeatureExtractor computes extra features for each input PSM |
| SequenceCoverageCalculator | Prints information about idXML files |
| SpecLibCreator | Creates with given data a .MSP format spectral library |
| SpectraSTSearchAdapter | This util provides an interface to the 'SEARCH' mode of the SpectraST program. All non-advanced parameters of the executable of SpectraST were translated into parameters of this util |
| RNPxlSearch | Annotate RNA to peptide crosslinks in MS/MS spectra |
| RNPxlXICFilter | Filters MS2 spectra based on XIC intensities in control and treatment. Used in RNPxl experiments to reduce candidate spectra |
| ERPairFinder | Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans |
| FeatureFinderMetaboIdent | Detects features in MS1 data corresponding to small molecule identifications |
| FeatureFinderSuperHirn | |
| UTILS_MetaboliteAdductDecharger | Decharges a feature map by clustering charge variants of metabolites to zero-charge entities |
| MultiplexResolver | Completes peptide multiplets and resolves conflicts within them |
| AccurateMassSearch | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
| MetaboliteSpectralMatcher | MetaboliteSpectralMatcher identify small molecules from tandem MS spectra |
| SiriusAdapter | De novo metabolite identification |
| CorrelateMassTraces | Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps |
| MRMPairFinder | Util which can be used to evaluate pairs of MRM experiments |
| OpenSwathDIAPreScoring | .. |
| OpenSwathFileSplitter | A tool for splitting a single SWATH / DIA file into a set of files, each containing one SWATH window (plus one file for the MS1 survey scans) |
| OpenSwathMzMLFileCacher | Serialize a spectra and/or chromatogram mzML file |
| OpenSwathRewriteToFeatureXML | Combines featureXML and mProphet tsv to FDR filtered featureXML |
| NucleicAcidSearchEngine | Matches tandem mass spectra to nucleic acid sequences |
| RNADigestor | Digests an RNA sequence database in-silico |
| RNAMassCalculator | Calculates masses and mass-to-charge ratios of RNA sequences |
| QCCalculator | Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file |
| QCEmbedder | This application is used to embed tables or plots generated externally as attachments to existing quality parameters in qcML files |
| QCExporter | Will extract several quality parameter from several run/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 | Will import several quality parameter from a tabular (text) format into a qcML file - counterpart to QCExporter |
| QCMerger | Merges two qcml files together |
| QCShrinker | This application is used to remove extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report |
| ClusterMassTraces | Cluster mass traces occurring in the same map together |
| DeMeanderize | Repairs MALDI experiments which were spotted line by line |
| ImageCreator | Transforms an LC-MS map into a png image |
| MassCalculator | Calculates masses and mass-to-charge ratios of peptide sequences |
| MetaProSIP | Performs proteinSIP on peptide features for elemental flux analysis |
| MSSimulator | A highly configurable simulator for mass spectrometry experiments |
| SvmTheoreticalSpectrumGeneratorTrainer | Trainer for SVM model as input for SvmTheoreticalSpectrumGenerator |
| TICCalculator | Calculates the TIC of a raw mass spectrometric file |
| MSstatsConverter | Converter to input for MSstats |
| IDDecoyProbability | Util to estimate probability of peptide hits |
| ►TOPP tutorial | |
| TOPP and OpenMS | |
| Introduction | |
| The views | |
| Display modes and view options | |
| Data analysis | |
| Data editing | |
| Hotkeys table | |
| Smoothing raw data | |
| Subtracting a baseline from a spectrum | |
| Picking peaks | |
| Feature detection on centroided data | |
| TOPP for Advanced Users | |
| ►General introduction | |
| INIFileEditor | Can be used to visually edit INI files of TOPP tools |
| INIUpdater | Update INI and TOPPAS files from previous versions of OpenMS/TOPP |
| File Handling | |
| Profile data processing | |
| Calibration | |
| Map alignment | |
| Feature detection | |
| Feature grouping | |
| Consensus peptide identification | |
| Peptide property prediction | |
| Quality Control | |
| Conversion between OpenMS XML formats and text formats | |
| ►TOPP documentation | |
| TOPPView | |
| TOPPAS | An assistant for GUI-driven TOPP workflow design |
| INIFileEditor | Can be used to visually edit INI files of TOPP tools |
| DTAExtractor | Extracts scans of an mzML file to several files in DTA format |
| FileConverter | Converts between different MS file formats |
| FileFilter | Extracts portions of the data from an mzML, featureXML or consensusXML file |
| FileInfo | Shows basic information about the data in an OpenMS readable file |
| FileMerger | Merges several files. Multiple output format supported, depending on input format |
| IDMerger | Merges several idXML files into one idXML file |
| IDRipper | IDRipper splits the protein/peptide identifications of an idXML file into several idXML files according their annotated file origin |
| IDFileConverter | Converts peptide/protein identification engine file formats |
| MapStatistics | Extract extended statistics on the features of a map for quality control |
| TargetedFileConverter | Converts different spectral libraries / transition files for targeted proteomics and metabolomics analysis |
| TextExporter | This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to text files |
| MzTabExporter | This application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to mzTab |
| BaselineFilter | Executes the top-hat filter to remove the baseline of an MS experiment |
| InternalCalibration | Performs an internal mass recalibration on an MS experiment |
| ExternalCalibration | Performs an mass recalibration on an MS experiment using an external calibration function |
| MapNormalizer | Normalizes peak intensities to the percentage of the maximum intensity in the HPLC-MS map |
| MassTraceExtractor | MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile |
| NoiseFilterGaussian | Executes a Gaussian filter to reduce the noise in an MS experiment |
| NoiseFilterSGolay | Executes a Savitzky Golay filter to reduce the noise in an MS experiment |
| PeakPickerHiRes | A tool for peak detection in profile data. Executes the peak picking with high_res algorithm |
| PeakPickerWavelet | A tool for peak detection in profile data. Executes the peak picking with the algorithm described in described in Lange et al. (2006) Proc. PSB-06 |
| PrecursorMassCorrector | Corrects the precursor entries of MS/MS spectra, by using MS1 information |
| HighResPrecursorMassCorrector | Corrects the precursor mz of high resolution data |
| Resampler | Resampler can be used to transform an LC/MS map into a resampled map |
| SpectraFilterBernNorm | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterMarkerMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterNLargest | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterNormalizer | Normalizes intensity of peak spectra |
| SpectraFilterParentPeakMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterScaler | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterSqrtMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterThresholdMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraFilterWindowMower | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
| SpectraMerger | Allows to add up several spectra |
| TOFCalibration | Performs an external calibration for tof spectra |
| Decharger | Decharges a feature map by clustering charge variants of a peptide to zero-charge entities |
| EICExtractor | Extracts EICs from an MS experiment, in order to quantify analytes at a given position |
| FeatureFinderCentroided | The feature detection application for quantitation (centroided) |
| FeatureFinderIdentification | Detects features in MS1 data based on peptide identifications |
| FeatureFinderIsotopeWavelet | The feature detection application for quantitation |
| FeatureFinderMetabo | FeatureFinderMetabo assembles metabolite features from singleton mass traces |
| FeatureFinderMRM | The feature detection application for quantitation |
| FeatureFinderMultiplex | Detects peptide pairs in LC-MS data and determines their relative abundance |
| IsobaricAnalyzer | Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment |
| ProteinQuantifier | Compute peptide and protein abundances from annotated feature/consensus maps or from identification results |
| ProteinResolver | A peptide-centric algorithm for protein inference |
| SeedListGenerator | Application to generate seed lists for feature detection |
| MetaProSIP | Performs proteinSIP on peptide features for elemental flux analysis |
| ProteomicsLFQ | |
| ConsensusMapNormalizer | Normalization of intensities in a set of maps using robust regression |
| MapAlignerIdentification | Corrects retention time distortions between maps, using information from peptides identified in different maps |
| MapAlignerTreeGuided | Corrects retention time distortions between maps, using information from peptides identified in different maps |
| MapAlignerPoseClustering | Corrects retention time distortions between maps, using a pose clustering approach |
| MapAlignerSpectrum | Corrects retention time distortions between maps by aligning spectra |
| MapRTTransformer | Applies retention time transformations to maps |
| FeatureLinkerLabeled | Groups corresponding isotope-labeled features in a feature map |
| ►FeatureLinkerUnlabeled | Groups corresponding features from multiple maps |
| FileConverter | Converts between different MS file formats |
| FeatureLinkerUnlabeledQT | Groups corresponding features from multiple maps using a QT clustering approach |
| FeatureLinkerUnlabeledKD | Group corresponding features across labelfree experiments |
| CometAdapter | Identifies peptides in MS/MS spectra via Comet |
| CompNovo | Performs a peptide/protein identification with the CompNovo engine |
| CompNovoCID | Performs a peptide/protein identification with the CompNovo engine |
| CruxAdapter | Identifies peptides in MS/MS spectra via Crux and tide-search |
| InspectAdapter | Identifies peptides in MS/MS spectra via Inspect |
| MascotAdapter | Identifies peptides in MS/MS spectra via Mascot |
| MascotAdapterOnline | Identifies peptides in MS/MS spectra via Mascot |
| ►MSGFPlusAdapter | Adapter for the MS-GF+ protein identification (database search) engine |
| TOPP for Advanced Users | |
| MyriMatchAdapter | Identifies peptides in MS/MS spectra via MyriMatch |
| ►OMSSAAdapter | Identifies peptides in MS/MS spectra via OMSSA (Open Mass Spectrometry Search Algorithm) |
| TOPP for Advanced Users | |
| PepNovoAdapter | Identifies peptides in MS/MS spectra via PepNovo |
| SpecLibSearcher | Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library |
| SimpleSearchEngine | Identifies peptides in MS/MS spectra |
| ►XTandemAdapter | Identifies peptides in MS/MS spectra via the search engine X! Tandem |
| TOPP for Advanced Users | |
| ConsensusID | Computes a consensus from results of multiple peptide identification engines |
| FalseDiscoveryRate | Tool to estimate the false discovery rate on peptide and protein level |
| FidoAdapter | Runs the protein inference engine Fido |
| IDConflictResolver | Resolves ambiguous annotations of features with peptide identifications |
| IDFilter | Filters peptide/protein identification results by different criteria |
| IDMapper | Assigns protein/peptide identifications to features or consensus features |
| IDPosteriorErrorProbability | Tool to estimate the probability of peptide hits to be incorrectly assigned |
| IDRTCalibration | Can be used to calibrate the RTs of peptide hits linearly to standards |
| LuciphorAdapter | Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data |
| ►PeptideIndexer | Refreshes the protein references for all peptide hits from an idXML file and adds target/decoy information |
| TOPP for Advanced Users | |
| PhosphoScoring | Tool to score phosphorylation sites of peptides |
| ProteinInference | Computes a protein identification score based on an aggregation of scores of identified peptides |
| PercolatorAdapter | PercolatorAdapter facilitates the input to, the call of and output integration of Percolator. Percolator (http://per-colator.com/) is a tool to apply semi-supervised learning for peptide identification from shotgun proteomics datasets |
| OpenSwathWorkflow | Complete workflow to run OpenSWATH |
| AssayGeneratorMetabo | Generates an assay library using DDA data (Metabolomics) |
| InclusionExclusionListCreator | A tool for creating inclusion and/or exclusion lists for LC-MS/MS |
| MRMMapper | MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) |
| MRMTransitionGroupPicker | Picks peaks in SRM/MRM chromatograms that belong to the same precursors |
| PrecursorIonSelector | A tool for precursor ion selection based on identification results |
| OpenSwathAnalyzer | Executes a peak-picking and scoring algorithm on MRM/SRM data |
| OpenSwathAssayGenerator | Generates filtered and optimized assays using TraML files |
| OpenSwathChromatogramExtractor | Extracts chromatograms (XICs) from a file containing spectra |
| OpenSwathConfidenceScoring | Computes confidence scores for OpenSwath results |
| OpenSwathDecoyGenerator | Generates decoys according to different models for a specific TraML |
| OpenSwathFeatureXMLToTSV | Converts a featureXML to a mProphet tsv |
| OpenSwathRTNormalizer | The OpenSwathRTNormalizer will find retention time peptides in data |
| PTModel | Used to train a model for the prediction of proteotypic peptides |
| PTPredict | This application is used to predict the likelihood of peptides to be proteotypic |
| RTModel | Used to train a model for peptide retention time prediction or peptide separation prediction |
| RTPredict | This application is used to predict retention times for peptides or peptide separation |
| QualityControl | Generates an mzTab file from various sources of a pipeline (mainly a ConsensusXML) which can be used for QC plots (e.g. via the R package 'PTX-QC') |
| GenericWrapper | Allows generically the wrapping of external tools |
| ExecutePipeline | Executes workflows created by TOPPAS |
| GNPSExport | Export MS/MS data in .MGF format for GNPS (http://gnps.ucsd.edu) |
| MaRaClusterAdapter | MaRaClusterAdapter facilitates the input to, the call of and output integration of MaRaCluster. MaRaCluster (https://github.com/statisticalbiotechnology/maracluster) is a tool to apply unsupervised clustering of ms2 spectra from shotgun proteomics datasets |
| ►TOPPAS tutorial | |
| General introduction | |
| User interface | |
| Examples | |
| INIFileEditor | Can be used to visually edit INI files of TOPP tools |
| ▼Installation on GNU/Linux | |
| Building OpenMS on GNU/Linux | |
| Installation on MacOS | |
| Building OpenMS on Mac OS X | |
| Installation on Windows | |
| ▼Building OpenMS on Windows | |
| External Code using OpenMS | |
| 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 crosslink identifications |
| MapAlignerBase | Base class for different MapAligner TOPP tools |
| FeatureLinkerBase | Base class for different FeatureLinker tools |
| Experimental List | |
| Improvements List | |
| Todo List | |
| Deprecated List | |
| Bug List | |
1.8.16
