Proteogenomics and Immunopeptidomics

Date 29 November - 1 December 2017
Speaker(s) Manfredo Quadroni, Markus Müller, Sylvain Pradervand, Christian Ahrens, Juergen Cox, Michal Bassani-Sternberg, David Gfeller, Roman Mylonas, Lionel Breuza
Cancellation deadline 15 Nov 2017
City Lausanne

This course is co-organised by the CUSO/StarOmics doctoral program. Priority is given to its members, but is open to everyone.


Proteogenomics is an area of research at the interface of proteomics and genomics. It can be used to improve gene models, to discover new protein coding regions, and to obtain information about which gene variants are translated to proteins. Immunopeptidomics studies the generation and presentation of immune peptides, which are of particular importance for immunotherapies. Both proteogenomics and immunopeptidomics rely on tandem mass spectrometry to identify and quantify peptides or proteins. Rapid advances in DNA and RNA sequencing methods and bioinformatics made it possible to build protein sequence databases customized for a specific sample. In combination with tandem mass spectrometry and MS/MS search software it provides a powerful tool to study genetic variants.


This course is addressed to all students/scientists interested in the subjects of proteomics, mass spectrometry and immunology. The level is intermediate, meaning that there are some prerequisites (see below).

Learning objectives

The participants will be intoduced to:

  • proteomics and mass spectrometry
  • DNA and RNA sequencing
  • proteogenomics
  • immunopeptidomics

At the end of the course, the participants are expected to be able to:

  • build proteogenomics databases
  • perform proteogenomics searches with MaxQuant and PEAKS
  • cluster HLA peptides using MixMHC


Knowledge / competencies
Basic knowledge of immunology (HLA, T-cell, etc) and basic computer skills (program install, but no programming) are required. Previous experience in proteomics is a plus.

You are required to bring your own laptop and to install MaxQuant, PEAKS software (more information later).


Registration is open on the Staromics website.

No registration fees for members of staromics, otherwise they are 150 CHF for academics. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set is set to 15/11/2017. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.


University of Lausanne, Génopode building, classroom 2020 (Metro M1 line, Sorge station).

Additional information

Coordination: Corinne Dentan (Staromics), Grégoire Rossier (SIB Training Group)

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For more information, please contact