Proteomics Data Analysis

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IMPORTANT DATES for this Course
Deadline for applications: September 5th 2022
Course date: September 12th - September 16th 2022

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.


Lennart Martens Lennart Martens is Full Professor of Systems Biology at Ghent University, group leader of the Computational Omics and Systems Biology (CompOmics) group at VIB, and Associate Director of the VIB-UGent C enter for Medical Biotechnology, all in Ghent, Belgium. He has been working in proteomics bioinformatics since his Master's degree, which focused on the computational interpretation of peptide mass spectra. He then worked as a software developer and framework architect for a software company for a few years, before returning to Ghent University to pursue a Ph.D. focused on proteomics and proteomics informatics. During this time, he worked on the development of high-throughput peptide centric proteomics techniques and on bioinformatics tools to support these new approaches. In 2003 he started the PRIDE proteomics database at the EBI as a Marie Curie fellow of the European Commission. After obtaining his PhD, he rejoined the PRIDE group at EBI, which he coordinated for several years before moving back to Ghent University to take up his current position. Prof. Martens has been elected to the Human Proteome Organisation (HUPO) Council in 2016, and to the HUPO Executive Board in 2017. He received the 2014 Prometheus Award for Research Excellence from Ghent University, and the 2015 'Juan Pablo Albar' Proteomics Pioneer Award from the European Proteomics Association (EUPA). An author on more than 200 peer-reviewed papers, he has also co- written two popular Wiley textbooks: Computational Methods for Mass Spectrometry Proteomics (ISBN: 978-0-470-51297-5), and Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (ISBN: 978-1-119-96400-1). Lennart_Martens Martens is the president of EUPA since December 2020.

Affiliation: Ghent University and VIB, Ghent, BE

Lieven Clement is an Associate Professor of Statistical Genomics at Ghent University, where he leads the statOmics Group. He is an expert in developing statistical methods and open source tools for differential omics data analysis. His research efforts resulted in numerous publications on novel methods and tools for, and applied research in omics data analysis. His lab is built around two strategic research pillars each connected to an omics domain: (single cell) transcriptomics and proteomics and he has a strong interest in leveraging his expertise to translational research. He also serves as a member of the core team that established a new Master of Science in Bioinformatics at Ghent University and as a board member of the Belgian Proteomics Association.

Affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, BE

Course description

Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering peptide and protein identification, quantification, and differential analysis. Moreover, more advanced experimental designs and blocking will also be introduced. The core focus will be on shotgun proteomics data, and quantification using label-free precursor peptide (MS1) ion intensities. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon returning from the course. You will also learn how to submit data to PRIDE/ProteomeXchange, which is a common requirement for publication in the field, and how to browse and reprocess publicly available data from online repositories. The course will thus provide a solid basis for beginners, but will also bring new perspectives to those already familiar with standard d ata interpretation procedures in proteomics. Note: This is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full.

Course Pre-requisites

The participants should have a basic knowledge about mass spectrometry based proteomics. Experience in analysing proteomics data is an advantage, but not mandatory. The course does not require advanced computer skills.

You will also be requested to watch the following videos before attending the course:


Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:July 20th 2022