Short courses / Workshops

All workshops / short courses will be held in the conference venue in building B4.1 on Sunday, 11 March, in the afternoon, prior to the opening of the EMSC. The events start at 1:30pm and will go until 4:30pm.

There is no fee for the courses, but a separate registration with the workshop organizers is required. Please click on the workshop title to register for the event.

The following six workshops/short courses will be offered:

Workshops / short courses:

1. Computational and bioinformatics tools for proteomics

Proteomics investigates the identity, quantity, spatial and time dependent distribution of proteins in biological systems in a comparative manner. Therefore, and due to the massive amounts of measured MS data, it is inevitable that the developed methods and tools provide quick and reliable interpretations.

This short course gives insight into several aspects of proteomics data processing by going through the basic workflow; that is i) database acquisition, ii) peptide matching, iii) protein identification and iv) protein quantification. We will introduce the following tools: MS-Angel, SearchGUI, PeptideShaker, Knime and PIA.

The short course is for users who already have basic knowledge in analytical proteomics. Attendees should be familiar with topics such as target-decoy approach and false discovery rate. Please note that the complete workshop is organized as a hands-on session. please bring your own (modern) laptop (min. requirements: dual-core 1.8GHz, 4GB main memory / better 8GB, 40GB HDD).

After registration, we will inform you with further details. The space is limited to 25 participants.

This short course is supported by ProFI, de.NBI and ELIXIR.

Organizers: Martin Eisenacher (Ruhr-Universität Bochum), Dominik Kopczynski (ISAS Dortmund), David Bouyssié (University of Toulouse)

2. Novel and established approaches to high-performance mass spectrometry imaging

The workshop will discuss the performance and relevance of alternative approaches in mass spectrometry imaging (MSI). Singular and hyphenated ion formation and detection principles will be discussed, in relation to the well-established approaches based on MALDI, DESI and SIMS. Besides informational richness and contents of the different MSI approaches, the practicability shall be a key parameter of a methodological overview and evaluation.  

Organizers: Bernhard Spengler (Justus-Liebig-Universität Giessen), Andreas Römpp (Universität Bayreuth)

3. Cross-linking and HDX-MS: Towards the study of interacting domains in biological complexes

This workshop presents two emerging methodologies based on mass dpectrometry in the context of structural biology research. It is now well establish that proteins carry out their function through interaction with other partners. Although important protein complex structures have been elucidated by traditional high resolution techniques such as X-crystallography or nuclear magnetic resonance, the requirement for large amounts of high purity homogeneous samples has limited their application and the emergence of recent mass dpectrometry-based technologies has gained strong interest in the community of structural biologists. In particular, strategies based on cross-linking and on H/D exchange combined with MS show a high potential for generating structural data on supramolecular topologies.

Basic information about cross-linking and HDX- MS strategies will be presented as well as technical obstacles related to interdependent choices of reagents, protocols and softwares. Cross-linker reactivities and their applications to study protein-protein or protein-nucleic acid interactions will be shown. The lectures are summarized here.

Organizer: Noelle Potier (Université de Strasbourg)

4. Synthetic Polymers: 1) MS towards the megadalton range, 2) Ion mobility MS

The workshop will discuss different technical approaches to characterize synthetic polymers in the megaDalton range, as well as strategies to assess conformational features of synthetic polymers in the gas phase using ion mobility and appropriate models for collision cross section determination.

Further details on the workshop and the lectures can be found here.

The workshop is for users who already have basic knowledge in mass spectrometry of synthetic polymers.

Organizer: Laurence Charles (Université de Aix-Marseille)

5. CE-MS coupling: new developments and applications

The workshop will focus on the latest instrumental developments and cutting-edge CE-MS applications for small molecules, proteomics and biotherapeutics.

The preliminary programme of the workshop can be found here.

Organizer: Yannis François (Université de Strasbourg)

6. Data analysis in metabolomics

This short course is aimed at explaining how to use the METASPACE and GNPS platforms for large scale data analysis in mass spectrometry (MS) based metabolomics experiments. METASPACE couples advanced bioinformatics with high performance cloud computing to provide MS based annotations of Imaging MS and LC-MS datasets. GNPS is an open-access knowledgebase for public sharing, processing, curation and annotation of tandem mass spectrometry datasets, combining molecular networking with a community driven spectral library. More information can be found here.

Organizers: Ivan Protsyuk, Andrew Palmer, Theodore Alexandrov (EMBL Heidelberg), Daniel Petras, Pieter Dorrestein (UC San Diego)

Vendor seminars

Six vendor lunch seminars are offered during the conference. Please register individually with the companies (click on the company name for registration or to obtain more information).