mmzdouc / FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.

Introduction

FERMO is a dashboard app for processing and analysis of LC-MS(/MS) data for Windows, macOS and Linux. In particular, FERMO can be used to integrate LC-MS(/MS) data with quantitative biological data and other metadata, to facilitate:

• prioritization of compounds likely responsible for bioactivity,
• detection of fold-changes between conditions,
• annotation of metabolites and their selection based on novelty,
• assessment of the chemical diversity of samples.

For more information, see our bioRxiv preprint.

Documentation

The online documentation is located at the FERMO Github Wiki. Among other information, it includes:

• Installation instructions for Windows, macOS, and Linux
• Information on prerequisites
• A quickstart guide

Support

FERMO is actively supported and developed software. Please use the issue tracker to report errors and malfunctions.

About

Citation

When using the tool in published research, please cite:

• Zdouc, M. M. and Bayona Maldonado, L. M. and Augustijn, H. E. and Soldatou, S. and de Jonge, Niek and Jaspars, M. and van Wezel, G. P. and Medema, M. H. and van der Hooft, J. J. J., "FERMO: a Dashboard for Streamlined Rationalized Prioritization of Molecular Features from Mass Spectrometry Data", bioRxiv 2022.12.21.521422

Dependencies

A list of dependencies can be found in requirements.txt.

License

FERMO is licensed under the MIT License.

For Developers

Contributing

For details on our code of conduct and the process for submitting pull requests to us, please read CONTRIBUTING.md.

Versioning

We use Semantic Versioning for versioning.

Authors

• Mitja M. Zdouc - lead developer -
• Hannah E. Augustijn - interface design -

See also the list of contributors who participated in this project.

Acknowledgments (in Alphabetical Order)

• Bayona Maldonado, Lina M. - beta testing
• Dell, Maria - beta testing
• van der Hooft, Justin J. J. - project supervision
• Iorio, Marianna - beta testing
• de Jonge, Niek - code review, beta testing
• Khatib, Soliman - beta testing
• Lund, George - beta testing
• Maffioli, Sonia - beta testing
• Medema, Marnix H. - project supervision
• Padva, Leo - beta testing
• Simone, Matteo - beta testing
• Soldatou, Sylvia - beta testing