Retrieve Mass Spectrometry Data from MetaboLights

August 25, 2026 · View on GitHub

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov :name status badge years in bioc license

This repository provides a backend for Spectra objects that represents and retrieves mass spectrometry (MS) data directly from metabolomics experiments deposited at the public MetaboLights repository. Mass spectrometry data files of an experiment are downloaded and cached locally using the BiocFileCache package.

Installation

The package can be installed from Bioconductor with

install.packages("BiocManager")
BiocManager::install("MsBackendMetaboLights")

🤝 Contributing

We appreciate contributions of all kinds — from bug fixes and tests to documentation and new format support.

If you're planning to contribute:

  1. Read our contribution guidelines
  2. Follow the RforMassSpectrometry style guide
  3. Fork the repo, create a branch, implement your changes, and submit a pull request

Funding information

Part of this work was funded by the European Union under the HORIZON-MSCA-2021 project 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks, by the Autonomous Province of Bolzano under the MetaRbolomics4Galaxy project (CUP: D53C25001030003) from the Joint Projects South Tyrol–Germany 2025 funding program and by the DFG grant no. 564004112.

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