OpenMS for Metabolomics

Many of the tools and algorithms provided by OpenMS are developed with both proteomics and metabolomics in mind. First you convert vendor-specific formats into an open community-driven format. You can then filter, centroid, and recalibrate your spectra. OpenMS provides tools that are specifically designed for the metabolite quantification and metabolite identification. All tools are available as nodes in the workflow engine KNIME. In addition the complete workflow for the analysis of non-targeted metabolomics data is also available as a plugin for Thermo Compound Discoverer.

Selected Tools

  • Import, export and conversion of vendor formats and several open community-driven formats (e.g. mzML, mzIdentML, mzQuantML, mzTab)
  • Peak picking
  • Baseline and noise filtering
  • Recalibration
  • Retention time alignment
  • Metabolite quantification
  • Metabolite identification based on
    • Accurate mass
    • Tandem mass spectra