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Bas van Breukelen

Bas van Breukelen, Ph.D.

Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht University / Netherlands Proteomics Centre
Group size: 5

1. What is the leading research theme in your group?
"Bioinformatics for proteomics research. Our work spans the whole range from processing the raw mass spectrometry data to final qualitative and quantitative analysis of the protein content. This requires a lot of technology development, as roughly every six months there is a new and improved mass spectrometer available, which calls for a new algorithm. We also develop technology focused on specific domains within proteomics, such as phosphoproteomics, which deals with phosphorylated peptides and phosphorylation pathways. We do basic research as well, for example into the evolution of structural motifs in proteins and the conservation of post-translational modifications, but most of our work is driven by biological questions of other groups."

2. With what type of groups or organisations do you collaborate most and why?
"Because we cover so many different activities, our collaborations are also really diverse. We work together with pharmaceutical companies, for example on identifying the proteins that bind to their compound of interest. Groups working the University Medical Centre here in Utrecht have questions on the protein content of patient samples. We also collaborate with groups that do basic research and with other proteomics and bioinformatics groups, among others the EBI, SIB and of course the NBIC/NPC platform. A particularly close collaboration we have with the group of Berend Snel, also here in Utrecht. Our work on evolution of structural motifs is an example."

3. From your research perspective, what are the main challenges in bioinformatics right now?
"Integrating the various omics-domains. If we succeed in ensuring homogeneity in data and interoperability between data sources then I see great opportunities for progress. Of course, this is a huge challenge. We should start small in my opinion, with two closely related fields working on data from the same source. Keep it simple and gradually add more complexity. We are currently thinking about ways to integrate proteomics and genomics data. One of the tasks of bioinformaticians is that they more actively explain to the researchers in the wet-labs how an experiment should be set up and executed to ensure the quality and usability of the data. Bioinformatics is not a tool to be dictated by the lab."

4. What is the most important task of a group leader?
"Keep the overview. You also have to act as an interpreter to 'translate' a biological problem into a bioinformatics question."

5. How would you describe the atmosphere in your group?
"Very pleasant. We are a small group, we all know what everyone is doing.  There is a lot of discussion and we help each other out. We are part of a much bigger group and I think we are appreciated. Bioinformaticians are sometimes seen as leeches who profit from the biologists' success, but I don't think that is the case here."

Text by Esther Thole.