AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples.
BaselineFilter -- Removes the baseline from profile spectra using a top-hat filter.
CVInspector -- A tool for visualization and validation of PSI mapping and CV files.
CompNovo -- Performs a de novo peptide identification using the CompNovo engine.
CompNovoCID -- Performs a de novo peptide identification using the CompNovo engine.
ConsensusID -- Computes a consensus identification from peptide identifications of several identification engines.
ConsensusMapNormalizer -- Normalizes maps of one consensusXML file.
DBExporter -- Exports data from an OpenMS database to a file.
DBImporter -- Imports data to an OpenMS database.
DTAExtractor -- Extracts spectra of an MS run file to several files in DTA format.
DeMeanderize -- Orders the spectra of MALDI spotting plates correctly.
Decharger -- Decharges and merges different feature charge variants of the same peptide.
DecoyDatabase -- Create decoy peptide databases from normal ones.
Digestor -- Digests a protein database in-silico.
DigestorMotif -- digests a protein database in-silico.
EICExtractor -- Extracts intensities from dedicates positions in a LC/MS map.
ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
ExecutePipeline -- Executes workflows created by TOPPAS.
FFEval -- Evaluation tool for feature detection algorithms.
FalseDiscoveryRate -- Estimates the false discovery rate on peptide and protein level using decoy searches.
FeatureFinderCentroided -- Detects two-dimensional features in LC-MS data.
FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data.
FeatureFinderMRM -- Detects two-dimensional features in LC-MS data.
FeatureFinderMetabo -- Assembles metabolite features from singleton mass traces.
FeatureFinderRaw -- Determination of peak ratios in LC-MS data.
FeatureLinkerLabeled -- Groups corresponding isotope-labeled features in a feature map.
FeatureLinkerUnlabeled -- Groups corresponding features from multiple maps.
FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple maps.
FileConverter -- Converts between different MS file formats.
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.
FuzzyDiff -- Compares two files, tolerating numeric differences.
GenericWrapper -- Allows the generic wrapping of external tools.
HighResPrecursorMassCorrector -- Corrects the precursor mz determined by the instrument software.
IDConflictResolver -- Resolves ambiguous annotations of features with peptide identifications.
IDExtractor -- Extracts 'n' peptides randomly or best 'n' from IdXML files.
IDFileConverter -- Converts identification engine file formats.
IDFilter -- Filters results from protein or peptide identification engines based on different criteria.
IDMapper -- Assigns protein/peptide identifications to features or consensus features.
IDMassAccuracy -- Calculates a distribution of the mass error from given mass spectra and IDs.
IDMerger -- Merges several protein/peptide identification files into one file.
IDPosteriorErrorProbability -- Estimates probabilities for incorreclty assigned peptide sequences and a set of search engine scores using a mixture model.
IDRTCalibration -- Can be used to calibrate RTs of peptide hits linearly to standards.
IDSplitter -- Splits protein/peptide identifications off of annotated data files.
INIFileEditor -- An editor for OpenMS configuration files.
INIUpdater -- Update INI and TOPPAS files to new OpenMS version.
ITRAQAnalyzer -- Calculates iTRAQ quantitative values for peptides.
IdXMLEvaluation -- Application that evaluates tps, tns, fps, and fns for an IdXML file with predicted RTs.
ImageCreator -- Transforms an LC/MS map into a PNG image.
InclusionExclusionListCreator -- Creates inclusion and/or exclusion lists.
InspectAdapter -- Annotates MS/MS spectra using Inspect.
InternalCalibration -- Applies an internal calibration.
LabeledEval -- Evaluation tool for isotope-labeled quantitation experiments.
MRMPairFinder -- Util which can be used to evaluate labeled pair ratios on MRM features.
MSSimulator -- A highly configurable simulator for mass spectrometry experiments.
MapAlignerIdentification -- Corrects retention time distortions between maps based on common peptide identifications.
MapAlignerPoseClustering -- Corrects retention time distortions between maps using a pose clustering approach.
MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment.
MapAlignmentEvaluation -- Evaluates alignment results against a ground truth.
MapNormalizer -- Normalizes peak intensities in an MS run.
MapRTTransformer -- Applies retention time transformations to maps.
MapStatistics -- Extract extended statistics on the features of a map for quality control.
MascotAdapter -- Annotates MS/MS spectra using Mascot.
MascotAdapterOnline -- Annotates MS/MS spectra using Mascot.
MassCalculator -- Calculates masses and mass-to-charge ratios of peptide sequences.
MassTraceExtractor -- Detects mass traces in centroided LC-MS data.
MzTabExporter -- Exports various XML formats to an mzTab file.
NoiseFilterGaussian -- Removes noise from profile spectra by using Gaussian filter.
NoiseFilterSGolay -- Removes noise from profile spectra by using a Savitzky Golay filter.
OMSSAAdapter -- Annotates MS/MS spectra using OMSSA.
PILISIdentification -- performs a peptide/protein identification with the PILIS engine.
PILISModelCV -- Perform a cross validation of the PILIS model parameters.
PILISModelTrainer -- Train the PILIS model with a given set of spectra and identifications.
PILISSpectraGenerator -- Generate spectra given a list of peptides and a PILIS model.
PTModel -- Trains a model for the prediction of proteotypic peptides from a training set.
PTPredict -- predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel.
PeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra.
PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra.
PepNovoAdapter -- Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.
PeptideIndexer -- Refreshes the protein references for all peptide hits.
PhosphoScoring -- Scores potential phosphorylation sites and therby tries to localize the most probable sites.
PrecursorIonSelector -- PrecursorIonSelector.
PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information.
ProteinInference -- Protein inference based on the number of identified peptides.
ProteinQuantifier -- Compute peptide and protein abundances.
RTModel -- Trains a model for the retention time prediction of peptides from a training set.
RTPredict -- Predicts retention times for peptides using a model trained by RTModel.
Resampler -- Transforms an LC/MS map into a resampled map or a PNG image.
SILACAnalyzer -- Determination of peak ratios in LC-MS data.
SeedListGenerator -- Generates seed lists for feature detection.
SemanticValidator -- SemanticValidator for analysisXML and mzML files.
SequenceCoverageCalculator -- Prints information about IdXML files.
SpecLibCreator -- Creates an MSP formated spectral library.
SpecLibSearcher -- Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra.
SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra.
SpectraFilterNLargest -- Applies thresholdfilter to peak spectra.
SpectraFilterNormalizer -- Applies thresholdfilter to peak spectra.
SpectraFilterParentPeakMower -- Applies thresholdfilter to peak spectra.
SpectraFilterScaler -- Applies thresholdfilter to peak spectra.
SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra.
SpectraFilterThresholdMower -- Applies thresholdfilter to peak spectra.
SpectraFilterWindowMower -- Applies thresholdfilter to peak spectra.
SpectraMerger -- Merges spectra (each MS level separately), increasing S/N ratios.
SvmTheoreticalSpectrumGeneratorTrainer -- Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator.
TOFCalibration -- Applies time of flight calibration.
TOPPAS -- An assistant for GUI-driven TOPP workflow design.
TOPPView -- A viewer for mass spectrometry data.
TextExporter -- Exports various XML formats to a text file.
TransformationEvaluation -- Applies a transformation to a range of values.
XMLValidator -- Validates XML files against an XSD schema.
XTandemAdapter -- Annotates MS/MS spectra using XTandem.
The program is documented fully in the Tutorials, that are packaged in openms-doc.
On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.
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