March 2 – 7 , 2008, Dagstuhl Seminar 08101

Computational Proteomics


Christian Huber (Universität Salzburg, AT)
Oliver Kohlbacher (Universität Tübingen, DE)
Michal Linial (The Hebrew University of Jerusalem, IL)
Katrin Marcus (Ruhr-Universität Bochum, DE)
Knut Reinert (FU Berlin, DE)

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The field of Computational Proteomics has grown rapidly and gained a lot of momentum over the last years. Computational Proteomics was previously a field with a small and specialized community. Over the last few years, however, it has been recognized by experimental groups, that the analysis of the increasingly complex proteomics studies has become intractable without efficient algorithms implemented in easy-to-use tools. Conversely, the computer science and bioinformatics communities started to realize the wealth of interesting problems in this area. Both sides are thus eager to come together and work on these problems. To initiate this close collaboration of researchers from different fields (biology, medical sciences, biochemistry, analytical chemistry, bioinformatics, and computer science), we need opportunities to bring both communities together in an inspiring and relaxed atmosphere. Past experience from our 2005 seminar has shown that Dagstuhl is an ideal place for this.

Currently, computational proteomics faces a number of challenges. The increasing speed and accuracy of the new instrument generation yields datasets that are up to an order of magnitude larger than datasets seen a few years ago. This implies new algorithmic techniques and data analysis capabilities. The computer science problems to be tackled range from data management, over optimization problems, to machine learning. On the experimental side, the development of high mass accuracy and better separation techniques pose new challenges.

The seminar brought together a mixed audience from proteomics and bioinformatics: At the beginning we took a pool showing that there were 10 people who declared themselves as “wet lab” and 26 as “computer science”. Moreover, there were 21 people “holding a PhD degree” and 15 “working on it”. We are happy to see that the communities really grow together.

The talks and discussions were arranged on a daily basis featuring related topics:

  • Systems Biology and novel experimental techniques.
  • Quantitative analysis.
  • Identification.
  • Pathway analysis and biomarkers.

In conclusion, the workshop was very successful. It sparked interesting discussions, research collaborations, several joint grant proposals (e.g. for the BMBF program QuantPro), and joint publications. Other publications sparked by the seminar will certainly follow in the near future. The seminar also initiated the implementation of a webpage for interchanging proteomics data ( The success of the seminar and the positive feedback of the participants encourage us to organize a follow-up for this style of meeting.

Dagstuhl Seminar Series


  • Interdisciplinary With Non-informatics-topic Bioinformatics


  • Bioinformatics
  • Biomedicine
  • Proteomics
  • Analytical chemistry


In the series Dagstuhl Reports each Dagstuhl Seminar and Dagstuhl Perspectives Workshop is documented. The seminar organizers, in cooperation with the collector, prepare a report that includes contributions from the participants' talks together with a summary of the seminar.


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Dagstuhl's Impact

Please inform us when a publication was published as a result from your seminar. These publications are listed in the category Dagstuhl's Impact and are presented on a special shelf on the ground floor of the library.


Furthermore, a comprehensive peer-reviewed collection of research papers can be published in the series Dagstuhl Follow-Ups.