From European Proteomics Academy
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Here we try to present a list of useful tutorials that present the basic principles of proteomics technologies.

Internal Tutorials

These are tutorials created by us (or our collaborators) especially for this page:

External Tutorials

MaxQuant/Perseus Tutorials

The documentation of MaxQuant and Perseus contains abundant teaching material on the interpretation of quantitative data and associated statistics.

The documentation of both tools can be found here.

Skyline Tutorials

The Skyline wiki provides several tutorials on how to use the software.

The complete list can be found here.

Compomics Tutorials

The Computational Omics and Systems Biology Group at the VIB-UGent provide tutorials using user-friendly proteomics bioinformatics tools, most importantly SearchGUI and PeptideShaker.

The complete list of tutorials can be found at https://compomics.com/bioinformatics-for-proteomics/.

Currently, they offer three tutorials:

  1. Identification techniques
  2. Functional analysis
  3. Data sharing


The Biocontainers website contains extensive tutorials on how to design containers for bioinformatic tools.

The documentation can be found here.


Galaxy-P has tutorials on how to run proteomics tools in Galaxy.

The tutorials can be found here.

Online Video Tutorials

Title Category Description
Pladipus Intermediate / Advanced Video tutorial on how to set a distributed computing system using Pladipus by Kenneth Verheggen.
Cross Linking Intermediate / Advanced Video tutorial on how to idenify cross linked peptides using ProteinProspector by Robert Chalkley.