Proteomics Informatics Workshop series

A series of three one-day workshops for PhD students and post-docs working in the field of proteomics using mass spectrometry

Topic and theme

A plethora of bioinformatics tools has been developed to mine mass spectrometry data in proteomics. While many of the commercial tools provide online and hands-on workshops at conferences, high quality, free tools are also available that allow the investigator to process MS data, and these often outperform commercial offerings. Unfortunately, there is a constant and currently incompletely met need for hands-on practical training with these tools in Belgium. Hands-on experience with over five different, state-of-the-art free software tools will assure its relevance to any researcher working with proteomics MS data. By offering three days, this workshop can cover all major components of a standard data analysis pipeline providing a coherent overview, as opposed to the standard scattered courses on single software tools. For this reason, priority will be given to students applying for the full 3-day workshop.

Organising and scientific committee (+ contact information)

This workshop is organized by the Belgian Proteomics Association (BePA)
Contact: Dr. Maarten Dhaenens, Secretary of the BePA,
Laboratory for Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, B-9000 Gent
Tel: +32 (0)9 264 83 56

  • Scientific Committee

- Prof. Dr. Ir. Sebastien Carpentier, docent KULeuven

Faculteit Bio-ingenieurswetenschappen, Afdeling Plantenbiotechniek, Willem Decroylaan 42 bus 2455- 3001 Leuven, België
Tel. +32(0)16-379311

- Prof. Dr. Lennart Martens, hoogleraar UGent

Faculteit Geneeskunde en Gezondheidswetenschappen, Vakgroep Biochemie
Tel. +32(0)9-2649358

- Prof. Dr. Ir. Lieven Clement, docent UGent

Faculteit Wetenschappen, Vakgroep Toegepaste Wiskunde, Informatica en statistiek
Tel. +32 (0)9 2644904


Wednesdays 27 April + 4 May + 11 May 2016

  • Wed 27 April: Proteomics identification

08:30 09:00 Registration
09:00 09:40 Search engines and peptide identification (Lennart Martens)
09:40 10:40 Hands-on: using multiple search engines in SearchGUI (Lennart Martens- Kenneth Verheggen)
10:40 11:00 Coffee break
11:00 11:40 Peptide identification quality control (Lennart Martens)
11:40 12:00 Protein inference (Lennart Martens)
12:00 13:00 Lunch
13:00 14:30 Hands on: processing search engine results in PeptideShaker (Lennart Martens - Kenneth Verheggen)
14:30 15:00 Coffee break
15:00 15:30 Quantification approaches and pitfalls in proteomics (Lennart Martens)
15:30 17:00 Hands on: Peptizer for validation and protein inference (Lennart Martens - Kenneth Verheggen)

  • Wed 04 May: Proteomics quantification and study design

08:30 09:00 Registration
09:00 09:40 Data analysis strategies for quantitative proteomics: normalization, summarization, imputation and statistical testing (Lieven Clement)
09:40 10:40 Hands-on: isotope-based protein quantification using MaxQuant-Perseus (Ludger Goeminne - Adriaan Sticker)
10:40 11:00 Coffee break
11:00 12:00 Hands-on: label-free protein quantification using MaxQuant-Perseus (Ludger Goeminne - Adriaan Sticker)
12:00 13:00 Lunch
13:00 13:30 Design and data analysis of experiments with more complex designs (Lieven Clement)
13:30 14:30 Hands-on: label-free protein quantification using MaxQuant-R (Lieven Clement - Ludger Goeminne - Adriaan Sticker)
14:30 15:00 Coffee break
15:00 15:30 Summarization vs peptide-based approaches in label-free quantitative proteomics: performance, pitfalls and data analysis guidelines (Lieven Clement)
15:30 17:00 Hands on: peptide-based linear models using MaxQuant-R (Lieven Clement - Ludger Goeminne - Adriaan Sticker)

  • Wed 11 May: Proteomics data annotation

08:30 09:00 Registration
09:00 09:40 Introduction: annotation in proteomics: a special focus on non-model species and gene redundancy (Sebastien Carpentier)
09:40 10:40 Gene enrichment (Ewaut Kissel - Sebastien Carpentier)
10:40 11:00 Coffee break
11:00 12:00 Cross species annotation OMA (Ewaut Kissel - Sebastien Carpentier)
12:00 13:00 Lunch
13:30 14 30 Pathway analysis (Ewaut Kissel - Sebastien Carpentier)
14:30 15:00 Coffee break
15:00 17:00 The use of cytoscape in proteomics: the protein inference problem and gene ontologie


PC Knooppunt, Faculty of Pharmaceutical Sciences (FFW), Ghent University, Ottergemsesteenweg 460, 9000 Gent


Free of charge for members of the Doctoral School of Life Sciences and Medicine


Evaluation criteria (doctoral training programme)

100% participation

Number of participants

Maximum 25