Metabolomics Workflow

../../_images/metams_workflow2024.svg

Workflow Overview

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 Availability

The workflow is available in GitHub: https://github.com/microbiomedata/metaMS

The container is available at Docker Hub (microbiomedata/metaMS): https://hub.docker.com/r/microbiomedata/metams

The python package is available on PyPi: https://pypi.org/project/metaMS/

The databases are available by request. Please contact NMDC (support@microbiomedata.org) for access.

Requirements for Execution

  • Docker Container Runtime

    or

  • Python Environment >= 3.10

  • Python Dependencies are listed on requirements.txt

Execution Details

Please refer to:

https://github.com/microbiomedata/metaMS#metams-installation

Hardware Requirements

  • To run this application, you need a processor with at least 2.0 GHz speed, 8GB of RAM, 10GB of free hard disk space

Workflow Dependencies

Software

  • CoreMS (2-clause BSD)

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

Database

Test datasets

https://github.com/microbiomedata/metaMS/tree/master/data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf

Inputs

  • Supported format for low resolution GC-MS data:
    • ANDI NetCDF for GC-MS (.cdf)

  • Fatty Acid Methyl Esters Calibration File:
    • ANDI NetCDF for GC-MS (.cdf) - C8 to C30

  • Parameters:
    • CoreMS Parameter File (.json)

    • MetaMS Parameter File (.json)

Outputs

  • Metabolites data-table
    • CSV, TAB-SEPARATED TXT

    • HDF: CoreMS HDF5 format

    • XLSX : Microsoft Excel

  • Workflow Metadata:
    • JSON

Version History

  • 3.1.0

Point of contact

Package maintainer: Yuri E. Corilo <corilo@pnnl.gov>