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 Galaxy servers
Introduction to Metabolomics
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Mass spectrometry imaging: Examining the spatial distribution of analytes
Mass spectrometry imaging: Finding differential analytes
Mass spectrometry: LC-MS analysis
Mass spectrometry: LC-MS data processing
Mass spectrometry: LC-MS preprocessing with XCMS
plain text tutorial

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.


This material is maintained by:

AvatarGildas Le CorguilléAvatarMélanie Peteraorcid logoAvatarMelanie 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:

AvatarYann GuittonAvatarMélanie Peteraorcid logoAvatarMelanie FöllAvatarJean-François MartinAvatarGildas Le CorguilléAvatarWorkflow4Metabolomics core teamAvatarCécile CanletAvatarJulien Saint-VanneAvatarMaren Stillger