OpenMS
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[detail level 12]
 How to write Commit messages
 pyOpenMS (Python bindings)
 MapAlignerBaseBase class for different MapAligner TOPP tools
 AccurateMassSearchAn algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB)
 AssayGeneratorMetaboGenerates an assay library using DDA data (Metabolomics)
 AssayGeneratorMetaboSiriusGenerates an assay library from SIRIUS fragmentation trees (Metabolomics)
 BaselineFilterExecutes the top-hat filter to remove the baseline of an MS experiment
 ClusterMassTracesCluster mass traces occurring in the same map together
 ClusterMassTracesByPrecursorIdentifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps
 CometAdapterIdentifies peptides in MS/MS spectra via Comet
 ConsensusIDComputes a consensus from results of multiple peptide identification engines
 ConsensusMapNormalizerNormalization of intensities in a set of maps using robust regression
 CVInspectorA tool for visualization and validation of PSI mapping and CV files
 DatabaseFilterThe DatabaseFilter tool filters a protein database in fasta format according to one or multiple filtering criteria
 DatabaseSuitabilityCalculates the suitability of a database which was used a for peptide identification search. Also reports the quality of LC-MS spectra
 DechargerDecharges a feature map by clustering charge variants of a peptide to zero-charge entities
 DecoyDatabaseCreate a decoy peptide database from standard FASTA databases
 DeMeanderizeRepairs MALDI experiments which were spotted line by line in a meandering pattern
 DigestorDigests a protein database in-silico
 DigestorMotifThis 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
 DTAExtractorExtracts scans of an mzML file to several files in DTA format
 EICExtractorExtracts EICs from an MS experiment, in order to quantify analytes at a given position
 EpifanyEPIFANY - 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
 ExecutePipelineExecutes workflows created by TOPPAS
 ExternalCalibrationPerforms an mass recalibration on an MS experiment using an external calibration function
 FalseDiscoveryRateTool to estimate the false discovery rate on peptide and protein level
 FeatureFinderCentroidedThe feature detection application for quantitation (centroided)
 FeatureFinderIdentificationDetects features in MS1 data based on peptide identifications
 FeatureFinderMetaboFeatureFinderMetabo assembles metabolite features from singleton mass traces
 FeatureFinderMetaboIdentDetects features in MS1 data corresponding to small molecule identifications
 FeatureFinderMultiplexDetects peptide pairs in LC-MS data and determines their relative abundance
 FeatureLinkerBaseBase class for different FeatureLinker tools
 FeatureLinkerLabeledGroups corresponding isotope-labeled features in a feature map
 FeatureLinkerUnlabeledGroups corresponding features from multiple maps
 FeatureLinkerUnlabeledKDGroup corresponding features across labelfree experiments
 FeatureLinkerUnlabeledQTGroups corresponding features from multiple maps using a QT clustering approach
 FileFilterExtracts portions of the data from an mzML, featureXML or consensusXML file
 FileInfoShows basic information about the data in an OpenMS readable file
 FileMergerMerges several files. Multiple output formats supported, depending on the input format
 FLASHDeconvFLASHDeconv performs ultrafast deconvolution of top down proteomics MS datasets. FLASHDeconv takes mzML file as input and outputs deconvolved feature list (.tsv) and deconvolved spectra files (.tsv, .mzML, .msalign, .ms1ft). FLASHDeconv uses FLASHDeconvAlgorithm for spectral level deconvolution and MassFeatureTracer to detect mass features. Also for MSn spectra, the precursor masses (not peak m/zs) should be determined and assigned in most cases. This assignment can be done by tracking MSn-1 spectra deconvolution information. Thus FLASHDeconv class keeps MSn-1 spectra deconvolution information for a certain period for precursor mass assignment in DeconvolvedSpectrum class. In case of FLASHIda runs, this precursor mass assignment is done by FLASHIda. Thus FLASHDeconv class simply parses the log file from FLASHIda runs and pass the parsed information to DeconvolvedSpectrum class
 FuzzyDiffCompares two files, tolerating numeric differences
 GenericWrapperAllows generically the wrapping of external tools
 HighResPrecursorMassCorrectorCorrects the precursor mz of high resolution data
 IDConflictResolverResolves ambiguous annotations of features with peptide identifications
 IDDecoyProbabilityUtil to estimate probability of peptide hits
 IDExtractorExtracts 'n' peptides randomly or best 'n' from idXML files
 IDFilterFilters peptide/protein identification results by different criteria
 IDMapperAssigns protein/peptide identifications to features or consensus features
 IDMergerMerges several idXML files into one idXML file
 IDPosteriorErrorProbabilityTool to estimate the probability of peptide hits to be incorrectly assigned
 IDRipperIDRipper splits the protein/peptide identifications of an idXML file into several idXML files according their annotated file origin
 IDRTCalibrationCan be used to calibrate the RTs of peptide hits linearly to standards
 IDScoreSwitcherSwitches between different scores of peptide hits (PSMs) or protein hits in identification data
 IDSplitterSplits protein/peptide identifications off of annotated data files
 ImageCreatorTransforms an LC-MS map into a png image
 INIUpdaterUpdate INI and TOPPAS files from previous versions of OpenMS/TOPP
 InternalCalibrationPerforms an internal mass recalibration on an MS experiment
 IonMobilityBinningSplits an mzML file with IonMobility frames into multiple mzML files by binning(merging) spectra by their IM values
 IsobaricAnalyzerExtracts and normalizes isobaric labeling information from an LC-MS/MS experiment
 JSONExporterConverts .oms (SQLite) files to JSON
 LuciphorAdapterAdapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data
 MapAlignerIdentificationCorrects retention time distortions between maps, using information from peptides identified in different maps
 MapAlignerPoseClusteringCorrects retention time distortions between maps, using a pose clustering approach
 MapAlignerTreeGuidedCorrects retention time distortions between maps, using information from peptides identified in different maps
 MapNormalizerNormalizes peak intensities to the percentage of the maximum intensity in the HPLC-MS map
 MapRTTransformerApplies retention time transformations to maps
 MapStatisticsExtract extended statistics on the features of a map for quality control
 MaRaClusterAdapterMaRaClusterAdapter 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
 MascotAdapterOnlineIdentifies peptides in MS/MS spectra via Mascot
 MassCalculatorCalculates masses and mass-to-charge ratios of peptide sequences
 MassTraceExtractorMassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile
 MetaboliteAdductDechargerDecharges a feature map by clustering charge variants of metabolites to zero-charge entities
 MetaboliteSpectralMatcherMetaboliteSpectralMatcher identifies small molecules from tandem MS spectra using a spectral library
 MetaProSIPPerforms proteinSIP on peptide features for elemental flux analysis
 MRMMapperMRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
 MRMPairFinderUtil which can be used to evaluate pairs of MRM experiments
 MRMTransitionGroupPickerPicks peaks in SRM/MRM chromatograms that belong to the same precursors
 MSFraggerAdapterPeptide Identification with MSFragger
 MSGFPlusAdapterAdapter for the MS-GF+ protein identification (database search) engine
 MultiplexResolverCompletes peptide multiplets and resolves conflicts within them
 MzMLSplitterSplits an mzML file into multiple parts
 NoiseFilterGaussianExecutes a Gaussian filter to reduce the noise in an MS experiment
 NoiseFilterSGolayExecutes a Savitzky Golay filter to reduce the noise in an MS experiment
 NovorAdapterNovoradapter for de novo sequencing from tandem mass spectrometry data
 NucleicAcidSearchEngineMatches tandem mass spectra to nucleic acid sequences
 OpenMSDatabasesInfoInformation about OpenMS' internal databases
 OpenMSInfoPrints configurations details of OpenMS (Version, Git hash, SIMD extensions, Multithreading), along with directories where auxilliary data like modifications (UniMOD), Enzymes etc are taken from
 OpenNuXLAnnotate NA to peptide crosslinks in MS/MS spectra
 OpenPepXLSearch for peptide pairs linked with a labeled cross-linker
 OpenSwathAnalyzerExecutes a peak-picking and scoring algorithm on MRM/SRM data
 OpenSwathAssayGeneratorGenerates filtered and optimized assays using TraML files
 OpenSwathChromatogramExtractorExtracts chromatograms (XICs) from a file containing spectra
 OpenSwathConfidenceScoringComputes confidence scores for OpenSwath results
 OpenSwathDecoyGeneratorGenerates decoys according to different models for a specific TraML
 OpenSwathDIAPreScoring..
 OpenSwathFeatureXMLToTSVConverts a featureXML to a mProphet tsv
 OpenSwathFileSplitterA 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)
 OpenSwathMzMLFileCacherSerialize a spectra and/or chromatogram mzML file
 OpenSwathRewriteToFeatureXMLCombines featureXML and mProphet tsv to FDR filtered featureXML
 OpenSwathRTNormalizerThe OpenSwathRTNormalizer will find retention time peptides in data
 OpenSwathWorkflowComplete workflow to run OpenSWATH
 PeakPickerHiResA tool for peak detection in profile data. Executes the peak picking with high_res algorithm
 PeakPickerIterativeA tool for peak detection in profile data. Executes the peak picking with high_res algorithm
 PeptideIndexerRefreshes the protein references for all peptide hits from an idXML file and adds target/decoy information
 PercolatorAdapterPercolatorAdapter facilitates the input to, the call of and output integration of Percolator. Percolator (http://percolator.ms/) is a tool to apply semi-supervised learning for peptide identification from shotgun proteomics datasets
 PhosphoScoringTool to score phosphorylation sites of peptides
 ProteinInferenceComputes a protein identification score based on an aggregation of scores of identified peptides
 ProteinQuantifierCompute peptide and protein abundances from annotated feature/consensus maps or from identification results
 ProteomicsLFQ
 PSMFeatureExtractorPSMFeatureExtractor computes extra features for each input PSM
 QCCalculatorCalculates basic quality parameters from MS experiments and compiles data for subsequent QC into a mzQC or qcML file
 QCEmbedderThis application is used to embed tables or plots generated externally as attachments to existing quality parameters in qcML files
 QCExporterWill extract several quality parameter from several run/sets from a qcML file into a tabular (text) format - counterpart to QCImporter
 QCExtractorExtracts a table attachment of a given quality parameter from a qcML file as tabular (text) format
 QCImporterWill import several quality parameter from a tabular (text) format into a qcML file - counterpart to QCExporter
 QCMergerMerges two qcml files together
 QCShrinkerThis application is used to remove extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report
 QualityControlGenerates 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 'PTXQC')
 ResamplerResampler can be used to transform an LC/MS map into a resampled map
 RNADigestorDigests an RNA sequence database in-silico
 RNAMassCalculatorCalculates masses, mass-to-charge ratios and sum formulas of RNA sequences
 RNPxlXICFilterFilters MS2 spectra based on XIC intensities in control and treatment. Used in RNPxl experiments to reduce candidate spectra
 SageAdapterIdentifies peptides in MS/MS spectra via sage
 SeedListGeneratorApplication to generate seed lists for feature detection
 SemanticValidatorSemanticValidator for XML files which can be semantically validated
 SequenceCoverageCalculatorPrints information about idXML files
 SimpleSearchEngineIdentifies peptides in MS/MS spectra
 SiriusExportDe novo metabolite identification
 SpectraFilterNLargestFilters the top Peaks in the given spectra according to a given schema/thresholdset
 SpectraFilterNormalizerScale intensities per spectrum to either sum to 1 or have a maximum of 1
 SpectraFilterThresholdMowerRemoves all peaks below an intensity threshold
 SpectraFilterWindowMowerRetains the highest peaks in a sliding or jumping window
 SpectraMergerAllows to add up several spectra
 SpectraSTSearchAdapterThis 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
 StaticModificationApplies a set of modifications to all PeptideIDs in an idXML file
 TargetedFileConverterConverts different spectral libraries / transition files for targeted proteomics and metabolomics analysis
 TextExporterThis application converts several OpenMS XML formats (featureXML, consensusXML, and idXML) to text files
 TICCalculatorCalculates the TIC of a raw mass spectrometric file
 TriqlerConverterConverter to input for Triqler
 XFDRCalculates false discovery rate estimates on crosslink identifications
 XMLValidatorValidates XML files against an XSD schema
 Todo List
 Improvements List
 Experimental List
 Deprecated List
 Bug List