Metabolomics Workflow (v2.1.0)


The gas chromatography-mass spectrometry (GC-MS) based metabolomics workflow (metaMS) has been developed by leveraging PNNL’s CoreMS software framework. The current software design allows for the orchestration of the metabolite characterization pipeline, i.e., signal noise reduction, m/z based Chromatogram Peak Deconvolution, abundance threshold calculation, peak picking, spectral similarity calculation and molecular search, similarity score calculation, and confidence filtering, all in a single step.

Workflow Diagram


Workflow Dependencies

Third party software

  • CoreMS (2-clause BSD)
  • Click (BSD 3-Clause “New” or “Revised” License)


  • PNNL GC-MS Spectral Database

Workflow Availability

The workflow is available in GitHub:

The container is available at Docker Hub (microbiomedata/metaMS):

The python package is available on PyPi:

The databases are available by request. Please contact NMDC ( for access.

Execution Details

Please refer to:


  • ANDI NetCDF for GC-MS (.cdf)
  • CoreMS Hierarchical Data Format (.hdf5)
  • CoreMS Parameter File (.JSON)
  • MetaMS Parameter File (.JSON)


  • Metabolites data-table
    • HDF: CoreMS HDF5 format
    • XLSX : Microsoft Excel
  • Workflow Metadata:
    • JSON

Requirements for Execution

  • Docker Container Runtime
  • Python Environment >= 3.6
  • Python Dependencies are listed on requirements.txt

Version History

  • 2.1.0

Point of contact

Package maintainer: Yuri E. Corilo <>