Retrieved 27 October QCImporter — Imports tables with quality control parameters into qcml files. XFDR — Calculates false discovery rate estimates on crosslink identifications. FeatureFinderSuperHirn — Finds mass spectrometric features in mass spectra. MultiplexResolver — Completes peptide multiplets and resolves conflicts within them. NoiseFilterGaussian — Removes noise from profile spectra by using Gaussian filter on uniform as well as non-uniform data. Since the inception of the project, a yearly OpenMS user meeting has been held at several universities where developers and users of the framework had the chance to present new features of OpenMS and direct, biological applications of OpenMS.
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November TOPP 1. MetaboliteAdductDecharger — Decharges and merges different feature charge variants of the same metabolite. IDScoreSwitcher — Switches between different scores of toopview or protein hits in identification data. IsobaricAnalyzer — Calculates isobaric quantitative values for peptides. QCCalculator — Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. OpenMS offers an infrastructure for the development of mass spectrometry- related software and powerful 2D and 3D visualization solutions.
Older version, still supported. RTModel — Trains a model for the retention time prediction of toppvview from a training set. SeedListGenerator — Generates seed lists for feature detection.
TOPPView: an open-source viewer for mass spectrometry data.
QCImporter — Imports tables with quality control parameters into qcml files. TransformationEvaluation — Applies a transformation to a range of values.
The program is documented fully in the Tutorialsthat are packaged in openms-doc. SpectraFilterScaler — Applies thresholdfilter to peak spectra. BMC Bioinformatics9: QCMerger — Merges two qcml files together.
FeatureLinkerUnlabeled — Groups corresponding features from multiple maps. ProteinQuantifier — Compute peptide and protein abundances.
ConsensusID — Computes a consensus of peptide identifications of several identification engines. PTModel — Trains a model for the prediction of proteotypic peptides from a training set. SpectraFilterBernNorm — To;pview thresholdfilter to peak spectra. PeakPickerWavelet — Finds mass spectrometric peaks in profile mass spectra. LabeledEval — Evaluation tool for isotope-labeled quantitation experiments. Pages using Infobox software with unknown parameters.
OpenMS – Open-source software for mass spectrometry analysis
This page was last edited on 26 Marchat Multiple tools were significantly improved with regard to memory and CPU performance. Support for Python bindings, performance improvements, Mascot 2.
OpenMS was originally released in in version 1. It transforms most of the OpenMS functionality into small command line tools that are the building blocks for more complex analysis pipelines.
Retrieved 4 July NoiseFilterGaussian — Removes noise from profile spectra by using Gaussian filter on uniform as well as non-uniform data. Among others, it provides algorithms for signal processing, feature tlppview including de-isotopingvisualization, map mapping and peptide identification.
LinuxWindowsOS X. PeptideIndexer — Refreshes the protein references for all peptide hits.