Natural Organic Matter Workflow


Direct Infusion Fourier Transform mass spectrometry (DI FT-MS) data undergoes signal processing and molecular formula assignment leveraging EMSL’s CoreMS framework. Raw time domain data is transformed into the m/z domain using Fourier Transform and Ledford equation. Data is denoised followed by peak picking, recalibration using an external reference list of known compounds, and searched against a dynamically generated molecular formula library with a defined molecular search space. The confidence scores for all the molecular formula candidates are calculated based on the mass accuracy and fine isotopic structure, and the best candidate assigned as the highest score.

Workflow Diagram


Workflow Dependencies

Third party software

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


  • CoreMS dynamic molecular database search and generator

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:


  • Supported format for Direct Infusion FT-MS data:
    • Thermo raw file (.raw)
    • Bruker raw file (.d)
    • Generic mass list in profile and/or centroid mode (inclusive of all delimiters types and Excel formats)
  • Calibration File:
    • Molecular Formula Reference (.ref)
  • Parameters:
    • CoreMS Parameter File (.json)
    • EnviroMS Parameter File (.json)


  • Molecular Formula Data-Table, containing m/z measuments, Peak height, Peak Area, Molecular Formula Identification, Ion Type, Confidence Score, etc.
    • HDF: CoreMS HDF5 format
    • XLSX : Microsoft Excel
  • Workflow Metadata:
    • JSON

Requirements for Execution

  • Docker Container Runtime or
  • Python Environment >= 3.8 and
  • Python Dependencies are listed on requirements.txt

Version History

  • 4.1.5

Point of contact

Package maintainer: Yuri E. Corilo <>