Metabolomics Workflow
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
Available at https://metabref.emsl.pnnl.gov/
Test datasets
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
Current version is 3.3.1
Point of contact
Package maintainer: Yuri E. Corilo <corilo@pnnl.gov>