August 23 – 28 , 2015, Dagstuhl Seminar 15351

Computational Mass Spectrometry


Rudolf Aebersold (ETH Zürich, CH)
Oliver Kohlbacher (Universität Tübingen, DE)
Olga Vitek (Northeastern University – Boston, US)

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Dagstuhl Report, Volume 5, Issue 8 Dagstuhl Report
Aims & Scope
List of Participants
Dagstuhl's Impact: Documents available



Mass Spectrometry (MS) is an extremely flexible analytical technique, with applications ranging from crime lab investigations to testing to disease biomarkers in a clinic. The publication of the first human genome in 2001 was a key event that lead to the application of mass spectrometry to map out the human proteome, and later the human metabolome; i.e. all the biomolecules encoded in the genome that constitute biological function. The result was the creation of a tremendous amount of spectrometric data and a dearth of tools for data analysis, motivating the development of computational tools. The tool developers came from several expert domains; life scientists applying mass spectrometry built tools to automate their new workflows, analytical chemists and engineers developing the instruments built software to analyze devise measurements; network and database infrastructure professionals built resources for storing and sharing data in the cloud, and bioinformaticians and statisticians developed algorithms and statistical methods for data analysis. There is an ongoing need for the different disciplines to learn each other's languages, make tools interoperable, and establish common goals for development.


The seminar 'Computational Mass Spectrometry' is a follow-up seminar to the successful Dagstuhl seminars on `Computational Proteomics' and 'Computational Mass Spectrometry' (05471, 08101 and 14371).

The seminar aimed at bringing together scientists from a wide range of backgrounds and identify open issues and future research directions in computational mass spectrometry.


Already on the first days the seminar resulted in very lively discussions. The time allotted to the introductory talks had to be expanded to account for this. The discussions sparked off during the introductory talks led to the formation of several working groups. These groups formed and re-formed on demand, also based on discussion on the previous evenings. Section 5 documents the discussions and results in these groups through the notes taken. Some of these discussion (e.g., the one on false discovery rates) was of interest to all participants and took place as plenary discussions in the large lecture hall. Other discussions were more focussed and thus had a smaller number of participants.

Some of the discussion will certainly lead to joint research participants. A first tangible outcome is a joint paper already accepted in the Journal of Proteome Research (L. Gatto, K. D. Hansen, M. R. Hoopmann, H. Hermjakob, O. Kohlbacher, A.Beyer, "Testing and validation of computational methods for mass spectrometry," on benchmarking and validating computational methods for mass spectrometry. This working group developed conceptual ideas for benchmarking algorithms and implemented a web-based repository holding ( benchmark datasets that will hopefully make comparison of algorithms more transparent in the future. We are confident that the discussions of other working groups and the contacts made during the evening hours in Dagstuhl will result in many more collaborations and publications in the future.

The field of computational mass spectrometry is rapidly evolving. Participants identified a wide range of challenges arising from technological developments already at the horizon but also from the broadening on the application side. We thus intend to revisit the field in the coming years in a Dagstuhl seminar again, most likely organized by different leaders of the field in order to account for these upcoming changes.

Summary text license
  Creative Commons BY 3.0 Unported license
  Rudolf Aebersold, Oliver Kohlbacher, and Olga Vitek

Dagstuhl Seminar Series


  • Bioinformatics


  • Bioinformatics
  • Computational mass spectrometry
  • Proteomics
  • Metabolomics
  • Glycomics


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.


Download overview leaflet (PDF).

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.