Here, we have made some of the Proteomics bioinformatics courses' materials available for you to access any time. The last edition of the Proteomics bioinformatics course ran in July 2025.

This set of materials goes through the basics of mass spectrometry (MS) and proteomics bioinformatics. The materials include: how to use search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists, and incorporation of information from molecular interaction and pathway databases.

This course is organised in association with the Vlaams Instituut voor Biotechnologie (VIB).

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Using these materials

Learning outcomes

After completing the course, participants will be able to:

• Use and understand bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
• Browse, search, submit, retrieve, and re-use proteomics data from widely used public proteomics data repositories
• Evaluate the strengths and weaknesses of several experimental and bioinformatics analysis approaches
• Use tools to perform functional annotation of lists of proteins

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Learning outcomes

After completing the course, you will be able to:

• Use and summarise bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
• Browse, search, submit, retrieve, and re-use proteomics data from widely used public proteomics data repositories
• Evaluate the strengths and weaknesses of several experimental and bioinformatics analysis approaches
• Use tools to perform functional annotation of lists of proteins

Material collection editors

• Piv Gopalasingam, EMBL-EBI
• Lennart Martens, Ghent University
• Juan Antonio Vizcaino, EMBL-EBI

DOI: 10.6019/TOL.ProtBioinformaticsMaterials-t.2022.00001.1