Proteogenomics and Immunopeptidomics

29 November - 1 December 2017

Ioannis Xenarios

Dr. Grégoire Rossier, UniL/SIB

Manfredo Quadroni, Markus Müller, Sylvain Pradervand, Christian Ahrens, Juergen Cox, Michal Bassani-Sternberg, David Gfeller, Roman Mylonas, Lionel Breuza

The objective of this course is to present a review of all applications of the still emerging Proteomics field (compared to genomics) and the bioinformatics analysis challenges addressed by the enormous amount of data generated. We will develop use cases in immunoproteomics and in diabete.

University of Lausanne, Génopode, room 2020 (UNIL-Sorge M1 line stop)

Map

Program

https://edu.sib.swiss/course/view.php?id=308

Overview

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.

Audience

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

Prerequisites

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.

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

Application

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.

Location

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

Additional information

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

See also: www.sib.swiss

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.

PhD students of StarOmics are eligible for reimbursement of incurred travel expenses by train (half-fare card, and 2nd class) and meals (up to 25 CHF). Please send the original tickets (no copies, except for the general abonnement) with the reimbursement form to Corinne Dentan (see: biologie.cuso.ch)

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