Training material to analyse Mass spectrometry data in Galaxy: Metabolomics (LCMS, FIAMS, GCMS, NMR) and imaging.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.


Before diving into this topic, we recommend you to have a look at:


Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Metabolomics
Mass spectrometry imaging: Examining the spatial distribution of analytes
Mass spectrometry imaging: Finding differential analytes
Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)
Mass spectrometry: LC-MS analysis
Mass spectrometry: LC-MS data processing
Mass spectrometry: LC-MS preprocessing with XCMS

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

Gildas Le Corguillé avatar Gildas Le CorguilléMélanie Petera avatar Mélanie Peteraorcid logoMelanie Föll avatar Melanie Föll

For any question related to this topic and the content, you can contact them or visit our Gitter channel.


This material was contributed to by:

Yann Guitton avatar Yann GuittonJean-François Martin avatar Jean-François MartinJulien Saint-Vanne avatar Julien Saint-Vanneorcid logoMatej Troják avatar Matej TrojákCécile Canlet avatar Cécile Canletorcid logoMaxim Skoryk avatar Maxim Skorykorcid logoHelge Hecht avatar Helge HechtWorkflow4Metabolomics core team avatar Workflow4Metabolomics core teamGildas Le Corguillé avatar Gildas Le CorguilléMélanie Petera avatar Mélanie PeteraMaren Stillger avatar Maren Stillgerorcid logoHelena Rasche avatar Helena Rascheorcid logoMelanie Föll avatar Melanie Föll


These individuals or organisations provided funding support for the development of this resource