Training material for proteomics workflows in Galaxy

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:



Start here if you are new to proteomic analysis in Galaxy.

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to proteomics, protein identification, quantification and statistical modelling

Protein identification and quantification

These tutorials cover protein identification and/or label-free and label based quantification from data dependent acquisition (DDA) and data independent acquisition (DIA).

Lesson Slides Hands-on Recordings Input dataset Workflows
DIA Analysis using OpenSwathWorkflow
Label-free data analysis using MaxQuant
Label-free versus Labelled - How to Choose Your Quantitation Method
Library Generation for DIA Analysis
MaxQuant and MSstats for the analysis of label-free data
Peptide and Protein ID using OpenMS tools
Peptide and Protein ID using SearchGUI and PeptideShaker
Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
Protein FASTA Database Handling

Postprocessing of proteomics data

These tutorial cover statistical analyses and visualizations after protein identification and quantification.

Lesson Slides Hands-on Recordings Input dataset Workflows
Annotating a protein list identified by LC-MS/MS experiments
Biomarker candidate identification
Secretome Prediction
Statistical analysis of DIA data

Special proteomics techniques

These tutorials focus on special techniques such as N-terminomics and mass spectrometry imaging.

Lesson Slides Hands-on Recordings Input dataset Workflows
Detection and quantitation of N-termini (degradomics) via N-TAILS
Mass spectrometry imaging: Loading and exploring MSI data

Multi-omics analyses

These tutorials combine proteomics with other -omics technologies such as transcriptomics.

Lesson Slides Hands-on Recordings Input dataset Workflows
Metaproteomics tutorial
Proteogenomics 1: Database Creation
Proteogenomics 2: Database Search
Proteogenomics 3: Novel peptide analysis
metaQuantome 1: Data creation
metaQuantome 2: Function
metaQuantome 3: Taxonomy

Prediction of peptide properties

These tutorials explain in-silico analyses of different peptide properties.

Lesson Slides Hands-on Recordings Input dataset Workflows
Machine Learning Modeling of Anticancer Peptides
Peptide Library Data Analysis

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.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoAvatarMelanie Föllorcid logoAvatarSubina Mehtaorcid logoAvatarPratik Jagtaporcid logoAvatarBjörn Grüning

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:

AvatarRay SajulgaAvatarValentin LouxAvatarKlemens FröhlichAvatarFlorian Christoph Siglochorcid logoAvatarJayadev Joshiorcid logoAvatarTimothy J. GriffinAvatarPraveen Kumarorcid logoAvatarClemens Blankorcid logoAvatarBjörn Grüningorcid logoAvatarPratik JagtapAvatarMarie Craneorcid logoAvatarMatthias Fahrnerorcid logoAvatarDaniel BlankenbergAvatarYves Vandenbrouckorcid logoAvatarMelanie FöllAvatarFlorence CombesAvatarJames JohnsonAvatarEmma LeithAvatarDavid Christianyorcid logoAvatarSubina Mehta


This material was funded by: