Skip to content

Downloading public metabolomics data

This tutorial explains how to download public mass spectral raw data from MetaboLights, Metabolomics Workbench, or MassIVE/GNPS through GNPS tooling.

There are three main ways to download data.

Download raw data file-by-file in the GNPS2 Dashboard/Pan-ReDU Metadata Dashboard

GNPS Dashboard Download

Download raw data file-by-file in the GNPS2 Dataset Explorer

GNPS Explorer Download

Download raw data in batch through our public data downloader, which requires just a few steps with some coding.

This can be done through our public data downloader, which requires just a few command line steps.

  1. Make sure you have Python and Git installed on your system.

  2. Clone the repository through your terminal by running:

git clone https://github.com/Wang-Bioinformatics-Lab/downloadpublicdata.git
  1. Navigate to the directory in your terminal with:
cd downloadpublicdata
  1. Install required packages with:
pip install -r requirements.txt
  1. Test if it works with:
python ./bin/download_public_data_usi.py ./data/test_download.tsv ./data/ ./data/summary.tsv
  1. Replace ./data/test_download.tsv with the path to a TSV file containing the USIs you want to download. An example file can be found here. This should download the raw data into the folder ./data/.

Note: By default, files are converted to .mzML format before the download. If you wish to download without conversion, you can use the --noconversion flag:

python ./bin/download_public_data_usi.py ./data/test_download.tsv ./data/ ./data/summary.tsv --noconversion

Further details can be found in the GitHub README.

Page Contributions

Yasin El Abiead (UCSD) and Mingxun Wang (UCR)