BePA Proteomics Summer School: What can proteomics do for you?

Target audience

Any researcher that is interested in proteins. As specified on the BePA website, this is very broad, including all life sciences, bio-engineering, archeology, art sciences,…


Many researchers use proteomics as a research tool, e.g. in medicine, veterinary sciences, bioengineering, biology, pharmaceutical sciences, ecology and even within art sciences. BePA (Belgian Proteomics Association, is organizing workshops for these users. A broad selection of proteomics experts from Ghent will go through the entire workflow from sample preparation, over data acquisition to data analysis. At the end of the course, attendees will better understand the dos and don’ts in proteomics and be able to design their own experiment in order to find an answer to their protein-related questions.

Topic & Objectives

The course will cover the complete workflow of a proteomics experiment. Because sample preparation protocols are dependent on the research question, the samples at hand, the data acquisition methodology and on the final data analysis approach, each lecturer will cross reference to other days in the course. In this way, attendees will understand that a proteomics workflow can yield an answer to many questions, but only if the experiment was properly designed. However, if feasible, we would also allow attendees to subscribe for only a part of the course, most relevant to their current interest.

The workshop will show (young) researchers what the capabilities of proteomics are. By focusing on the different steps of a robust experimental design, they will learn the shortest route to the answer to their biological questions on proteins. Students that will defend their FWO scholarship application will have the perfect preparation, those in the final state of their PhD will fill the gaps they need for their PhD defence. Attendees will in no way become experts in proteomics or mass spectrometry, but when they collaborate with a dedicated (BePA) proteomics lab this course will teach them the language to communicate and think along.

Dates & venue:

20-23 September, UGent VIB Research Building FSVMII, Zwijnaarde.


DAY 1: experimental design Sample preparation techniques and (BDV, MD, FI, LC, GM, KG)

DAY 2: Data acquisition strategies (MD, FI, KG, BDV)

DAY 3: Data analysis: identification in DDA and DIA (MD, LM, GM, KG, FI)

DAY 4: Data analysis: quantification in DDA and DIA (LC, LM, MD)



Maarten Dhaenens (MD): Dr. Dhaenens has worked on MS in proteomics for 15 years. As founder of the ProGenTomics ( service lab he has experience in applying proteomics in very heterogeneous biological contexts. Together with his presidency for the European Young Proteomics Investigators Club ( and managing editor of the EuPA Open Proteomics Elsevier journal he recognized the need for more elaborate teaching on this widely applied analytical field. As current president of the Belgian Proteomics Association he helped initiate the current course.

Kris Gevaert (KG): Dr. Gevaert has close to 25 years of experience in the field of proteomics and thus far (co-)authored over 300 papers. He is a senior full professor at UGent, heads the Department of Biomolecular Medicine, is a VIB group leader, Associate Director of the VIB-UGent Center for Medical Biotechnology and scientific advisor of the VIB Proteomics Core. His group has developed and implemented novel proteomic technologies with a focus on protein modifications.

Gerben Menschaert (GM): After obtaining my Master’s degree in 1998, I worked for several years in pharmaceutical and biotech companies (Janssens Pharmaceutica & deVGen) as a bioinformatician. In 2006 I decided to “start over” in an academic setting. I joined the BioBix lab (Lab of Bioinformatics and Computational Genomics, Faculty of Bioscience Engineering, Ghent University) and did my PhD within the frame of a Strategic Fundamental Research Project (IWT-SBO) on Functional Peptidomics, a cross-university collaboration between groups of the University of Ghent, University of Leuven and Antwerp University. Afterwards I worked as a postdoctoral researcher in both the BioBix lab and Prometa (Interfaculty Centre for Proteomics and Metabolomics, KULeuven) and was granted a postdoctoral fellowship from the FWO (The Research Foundation Flanders) in 2012. In 2013 I stayed as a visiting scientist at the New York University Langone Medical Center (US), in the lab of Prof. David Fenyö, focussing on proteogenomics. Later in 2016, I was also granted a ½ year stay at the Queensland Univeristy, Brisbane, Australia, collaborating with Prof. Joseph Rothnagel on SEPs (short ORF-encoded polypeptides).

Currently, my main research focus is to combine different high throughput technologies and to integrate resulting information to address different biological questions, this in strong collaboration with partners such as NXTGNT and VIB-Ugent Center for Medical Biotechnology.

Francis Impens (FI): Francis Impens obtained his PhD in Biomedical Sciences at UGent in 2010 specializing in the field of MS-based proteomics. He then moved to the Pasteur Institute in Paris for a 4-year postdoc applying his proteomics expertise to study bacterial infection. In 2015, he moved back to Ghent and was appointed Head of the VIB Proteomics Core facility. Supported by an Odysseus starting grant he started his own research at UGent in 2016 and he was appointed Assistant Professor in 2018.

Lennart Martens (LM): From 2000 until 2002, Dr. Martens worked as framework architect for Sydney-Tristar Development Company, where he received the Company Achievement Award in 2001. In 2002, he returned to Ghent University to pursue a Ph.D. focused on proteomics informatics. As a PhD student, he developed several bioinformatics tools to support high-throughput, peptide centric proteomics, and in 2003 he conceived and developed the first version of the PRIDE database at EMBL-EBI as a Marie Curie fellow of the European Commission. After his Ph.D. in Sciences: Biotechnology from Ghent University in 2006, he rejoined the PRIDE team at EMBL-EBI and became PRIDE Group Coordinator in 2007. Dr. Martens pioneered the orthogonal re-use of large-scale proteomics data while at EMBL-EBI. In 2009, Dr. Martens returned Ghent University as Professor of Systems Biology. Dr. Martens teaches proteomics at many workshops around the world every year, and is a co-organizer of several highly acclaimed courses in Belgium and abroad.

Sven Eyckerman (SE):

  • PhD: Ghent Univ., Ghent, Belgium, 2002
  • Postdoc: Swiss Inst. for Experimental Cancer Res. (ISREC), Lausanne, Switzerland, 2004-06
  • Sr Scientist: Pronota NV, Ghent, Belgium, 2006-09
  • Postdoc: VIB, Jan Tavernier and Kris Gevaert Lab, Ghent, 2008-14
  • VIB Expert Scientist since January 2015​

Bart Devreese (BD):

  • Phd Ghent University 1997
  • Professor in Biochemistry since 2002

Bart Devreese pioneered the use of biomolecular mass spectrometry for protein and proteomics analysis since 1991. He is mainly engaged in the study of virulence mechanisms of opportunistic pathogens.  Since 2018, he joined the laboratory of microbiology to include his expertise in functional microbiology. He is author and co-author of more than 300 A1 papers in the broad field of analytical biochemistry and proteomics. He coordinates the Ghent University proteomics expertise center Proteogent.

Lieven Clement (LC): Since 2007, Lieven Clement’s research focusses on Genomics and Statistical Bioinformatics problems. In particular he developed statistical data analysis methods for microarrays, digital PCR, next-generation sequencing, and mass spectrometry based proteomics. 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 three strategic research pillars each connected to an omics domain: (meta)genomics, (single cell) transcriptomics and proteomics. He is also keen on leveraging his expertise in experimental design, omics data analysis and integration to researchers in the life science and to translational research.

Teaching methods

Teaching and presentations: 15 hours

Interactive workshop (on data analysis): 15 hours

Throughout the workshop, attendees will be allowed to bring forward their own research question in order to discuss the methodological opportunities available within the field. Teaching material that will be available to the participants: Slides and software.

Evaluation criteria

As for the 2016, 2018 and 2019 workshop, attendance will be monitored and reported back to the promotors.

More information