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pyOpenMS (Python bindings) | |
MapAlignerBase | Base class for different MapAligner TOPP tools |
AccurateMassSearch | An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB) |
AssayGeneratorMetabo | Generates an assay library using DDA data (Metabolomics) |
AssayGeneratorMetaboSirius | Generates an assay library from SIRIUS fragmentation trees (Metabolomics) |
BaselineFilter | Executes the top-hat filter to remove the baseline of an MS experiment |
ClusterMassTraces | Cluster mass traces occurring in the same map together |
ClusterMassTracesByPrecursor | Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps |
CometAdapter | Identifies peptides in MS/MS spectra via Comet |
ConsensusID | Computes a consensus from results of multiple peptide identification engines |
ConsensusMapNormalizer | Normalization of intensities in a set of maps using robust regression |
CVInspector | A tool for visualization and validation of PSI mapping and CV files |
DatabaseFilter | The DatabaseFilter tool filters a protein database in fasta format according to one or multiple filtering criteria |
DatabaseSuitability | Calculates the suitability of a database which was used a for peptide identification search. Also reports the quality of LC-MS spectra |
Decharger | Decharges a feature map by clustering charge variants of a peptide to zero-charge entities |
DecoyDatabase | Create a decoy peptide database from standard FASTA databases |
DeMeanderize | Repairs MALDI experiments which were spotted line by line in a meandering pattern |
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 |
DTAExtractor | Extracts scans of an mzML file to several files in DTA format |
EICExtractor | Extracts EICs from an MS experiment, in order to quantify analytes at a given position |
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 |
ExecutePipeline | Executes workflows created by TOPPAS |
ExternalCalibration | Performs an mass recalibration on an MS experiment using an external calibration function |
FalseDiscoveryRate | Tool to estimate the false discovery rate on peptide and protein level |
FeatureFinderCentroided | The feature detection application for quantitation (centroided) |
FeatureFinderIdentification | Detects features in MS1 data based on peptide identifications |
FeatureFinderMetabo | FeatureFinderMetabo assembles metabolite features from singleton mass traces |
FeatureFinderMetaboIdent | Detects features in MS1 data corresponding to small molecule identifications |
FeatureFinderMultiplex | Detects peptide pairs in LC-MS data and determines their relative abundance |
FeatureLinkerBase | Base class for different FeatureLinker tools |
FeatureLinkerLabeled | Groups corresponding isotope-labeled features in a feature map |
►FeatureLinkerUnlabeled | Groups corresponding features from multiple maps |
FileConverter | Converts between different MS file formats |
FeatureLinkerUnlabeledKD | Group corresponding features across labelfree experiments |
FeatureLinkerUnlabeledQT | Groups corresponding features from multiple maps using a QT clustering approach |
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 formats supported, depending on the input format |
FLASHDeconv | FLASHDeconv 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 |
FuzzyDiff | Compares two files, tolerating numeric differences |
GenericWrapper | Allows generically the wrapping of external tools |
HighResPrecursorMassCorrector | Corrects the precursor mz of high resolution data |
IDConflictResolver | Resolves ambiguous annotations of features with peptide identifications |
IDDecoyProbability | Util to estimate probability of peptide hits |
IDExtractor | Extracts 'n' peptides randomly or best 'n' from idXML files |
IDFilter | Filters peptide/protein identification results by different criteria |
IDMapper | Assigns protein/peptide identifications to features or consensus features |
IDMerger | Merges several idXML files into one idXML file |
IDPosteriorErrorProbability | Tool to estimate the probability of peptide hits to be incorrectly assigned |
IDRipper | IDRipper splits the protein/peptide identifications of an idXML file into several idXML files according their annotated file origin |
IDRTCalibration | Can be used to calibrate the RTs of peptide hits linearly to standards |
IDScoreSwitcher | Switches between different scores of peptide hits (PSMs) or protein hits in identification data |
IDSplitter | Splits protein/peptide identifications off of annotated data files |
ImageCreator | Transforms an LC-MS map into a png image |
INIUpdater | Update INI and TOPPAS files from previous versions of OpenMS/TOPP |
InternalCalibration | Performs an internal mass recalibration on an MS experiment |
IonMobilityBinning | Splits an mzML file with IonMobility frames into multiple mzML files by binning(merging) spectra by their IM values |
IsobaricAnalyzer | Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment |
JSONExporter | Converts .oms (SQLite) files to JSON |
LuciphorAdapter | Adapter for the LuciPHOr2: a site localisation tool of generic post-translational modifications from tandem mass spectrometry data |
MapAlignerIdentification | 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 |
MapAlignerTreeGuided | Corrects retention time distortions between maps, using information from peptides identified in different maps |
MapNormalizer | Normalizes peak intensities to the percentage of the maximum intensity in the HPLC-MS map |
MapRTTransformer | Applies retention time transformations to maps |
MapStatistics | Extract extended statistics on the features of a map for quality control |
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 |
MascotAdapterOnline | Identifies peptides in MS/MS spectra via Mascot |
MassCalculator | Calculates masses and mass-to-charge ratios of peptide sequences |
MassTraceExtractor | MassTraceExtractor extracts mass traces from a MSExperiment map and stores them into a FeatureXMLFile |
MetaboliteAdductDecharger | Decharges a feature map by clustering charge variants of metabolites to zero-charge entities |
MetaboliteSpectralMatcher | MetaboliteSpectralMatcher identifies small molecules from tandem MS spectra using a spectral library |
MetaProSIP | Performs proteinSIP on peptide features for elemental flux analysis |
MRMMapper | MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) |
MRMPairFinder | Util which can be used to evaluate pairs of MRM experiments |
MRMTransitionGroupPicker | Picks peaks in SRM/MRM chromatograms that belong to the same precursors |
MSFraggerAdapter | Peptide Identification with MSFragger |
MSGFPlusAdapter | Adapter for the MS-GF+ protein identification (database search) engine |
MultiplexResolver | Completes peptide multiplets and resolves conflicts within them |
MzMLSplitter | Splits an mzML file into multiple parts |
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 |
NovorAdapter | Novoradapter for de novo sequencing from tandem mass spectrometry data |
NucleicAcidSearchEngine | Matches tandem mass spectra to nucleic acid sequences |
OpenMSDatabasesInfo | Information about OpenMS' internal databases |
OpenMSInfo | Prints configurations details of OpenMS (Version, Git hash, SIMD extensions, Multithreading), along with directories where auxilliary data like modifications (UniMOD), Enzymes etc are taken from |
OpenNuXL | Annotate NA to peptide crosslinks in MS/MS spectra |
OpenPepXL | Search for peptide pairs linked with a labeled cross-linker |
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 |
OpenSwathDIAPreScoring | .. |
OpenSwathFeatureXMLToTSV | Converts a featureXML to a mProphet tsv |
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 |
OpenSwathRTNormalizer | The OpenSwathRTNormalizer will find retention time peptides in data |
OpenSwathWorkflow | Complete workflow to run OpenSWATH |
PeakPickerHiRes | 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 |
PeptideIndexer | Refreshes the protein references for all peptide hits from an idXML file and adds target/decoy information |
PercolatorAdapter | PercolatorAdapter 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 |
PhosphoScoring | Tool to score phosphorylation sites of peptides |
ProteinInference | Computes a protein identification score based on an aggregation of scores of identified peptides |
ProteinQuantifier | Compute peptide and protein abundances from annotated feature/consensus maps or from identification results |
ProteomicsLFQ | |
PSMFeatureExtractor | PSMFeatureExtractor computes extra features for each input PSM |
QCCalculator | Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a mzQC or 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 |
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 'PTXQC') |
Resampler | Resampler can be used to transform an LC/MS map into a resampled map |
RNADigestor | Digests an RNA sequence database in-silico |
RNAMassCalculator | Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences |
RNPxlXICFilter | Filters MS2 spectra based on XIC intensities in control and treatment. Used in RNPxl experiments to reduce candidate spectra |
SageAdapter | Identifies peptides in MS/MS spectra via sage |
SeedListGenerator | Application to generate seed lists for feature detection |
SemanticValidator | SemanticValidator for XML files which can be semantically validated |
SequenceCoverageCalculator | Prints information about idXML files |
SimpleSearchEngine | Identifies peptides in MS/MS spectra |
SiriusExport | De novo metabolite identification |
SpectraFilterNLargest | Filters the top Peaks in the given spectra according to a given schema/thresholdset |
SpectraFilterNormalizer | Scale intensities per spectrum to either sum to 1 or have a maximum of 1 |
SpectraFilterThresholdMower | Removes all peaks below an intensity threshold |
SpectraFilterWindowMower | Retains the highest peaks in a sliding or jumping window |
SpectraMerger | Allows to add up several spectra |
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 |
StaticModification | Applies a set of modifications to all PeptideIDs in an idXML file |
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 |
TICCalculator | Calculates the TIC of a raw mass spectrometric file |
TriqlerConverter | Converter to input for Triqler |
XFDR | Calculates false discovery rate estimates on crosslink identifications |
XMLValidator | Validates XML files against an XSD schema |
Todo List | |
Improvements List | |
Experimental List | |
Deprecated List | |
Bug List | |