Welcome to the Galaxy Mass Spectrometry Community!
An Open and Collaborative Community
We are a vibrant and inclusive network of researchers, developers, and trainers dedicated to advancing the fields of proteomics, metabolomics, exposomics and everything mass spec! Our community is committed to fostering open, reproducible, and accessible research through the use of Galaxy.
Our Mission
We believe in the power of collaboration and the importance of sharing knowledge.
Our mission is to:
- develop a set of well-documented and tested tools for the analysis of mass spectrometry data (both LC-MS/MS and GC-MS/MS),
- support researchers in their quest to understand complex biological systems using the MS. We provide workflows for various -omics to analyze complex MS data,
- provide comprehensive training materials describing such tools and workflows,
- facilitate a collaboration across pipelines and tools,
- conduct a research in an open and reproducible manner.
How do we function?
Meetings We meet every 2-3 months. There are two meetings in one day, one for the EU and one for AU time zone - you can choose the one that suits you more or join both!
Notes We keep rolling notes on a googledoc and monitor our work in a github project.
Chat Forum We have a chat forum on Matrix, where you can discuss news and ideas or ask for a help.
Join Us!
We invite you to become a part of our community! Whether you are a seasoned researcher or just starting, there are numerous opportunities to connect, learn, and contribute. Everybody with an interest in mass spectrometry is welcome!
Follow us on Twitter
I would like to...
... analyze my MS data!
You can start with the introduction to proteomics or introduction to metabolomics. Then follow with other tutorials: analysis of proteomic or metabolomic data in Galaxy.
Also, the GalaxyP team provides slides to conference talks or materials from workshops.
... learn more about Galaxy!
If you are completely new to Galaxy, these two tutorials are great point to start!
... develop new tools!
We keep all the source code on Github:
- General Galaxy repository.
- Github repository for proteomics tools
- Github repository for metabolomics tools from workflow4metabolomics
- GitHub repository for functional exposomics at RECETOX.
To start with the new tools development, check out the development training materials
... contribute to trainings!
If you would like to create new training materials or hold a training at your institute - we obviously have a training for that!
... participate in events!
Events related to MS data processing will be published here.
Important links
Meeting Notes doc <--- There's a section here called 'New here?' that gives tips on how to start contributing as well!
Recent publications
- Hecht, H., Rojas, W. Y., Ahmad, Z., Křenek, A., Klánová, J., & Price, E. J. (2024). Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals. Analytical Chemistry, 96(33), 13652–13662. link
- Galvis, J., Guyon, J., Dartigues, B., Hecht, H., Grüning, B., Specque, F., Soueidan, H., Karkar, S., Daubon, T., & Nikolski, M. (2024). DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data. Bioinformatics, 40(5). link
- Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19. Bihani S et al. (2024) doi: 10.1007/978-1-0716-3910-8_15. link
- An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. Kruk et al. (2024) doi: 10.1128/msystems.00929-23. link
- A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. Do et al. (2024) doi: 10.1128/msphere.00793-23. link
- The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Galaxy Community (2024). doi: 10.1093/nar/gkae410. link
- The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020) Jagtap et al. (2023) doi: 10.7171/3fc1f5fe.a058bad4. link
- A Galaxy of informatics resources for MS-based proteomics. Mehta et al. (2023). doi: 10.1080/14789450.2023.2265062. link
- Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics. Guitton et al. (2017) doi: 10.1016/j.biocel.2017.07.002. link
Key words
Mass Spectrometry Proteomics Metabolomics Data-dependent acquisition Data-independent acquisition Metaproteomics Proteogenomics Exposomics ELIXIR EIRENE