Volume

Dagstuhl Seminar Proceedings, Volume 8101

Publication Details

  • published at: 2008-12-22
  • Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik

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Document
DOI: 10.4230/DagSemProc.08101.1
08101 Abstracts Collection – Computational Proteomics

Authors: Knut Reinert, Christian Huber, Kathrin Marcus, Michal Linial, and Oliver Kohlbacher

Abstract
The second Dagstuhl Seminar on emph{Computational Proteomics} took place from March 3rd to 7th, 2008 in Schloss Dagstuhl--Leibniz Center for Informatics. This highly international meeting brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface between experiment and theory. This interdisciplinary exchange covered a wide range of topics, from new experimental methods resulting in more complex data we will have to expect in the future to purely theoretical studies of what level of experimental accuracy is required in order to solve certain problems. A particular focus was also on the application side, where the participants discussed more complex experimental methodologies that are enabled by more sophisticated computational techniques. Quantitative aspects of protein expression analysis as well as posttranslational modifications in the context of disease development and diagnosis were discussed. The seminar sparked a number of new ideas and collaborations and has resulted in several joint grant applications and paper submissions. This paper describes the seminar topics, its goals and results. The executive summary is followed by the abstracts of the presentations given. Links to extended abstracts or full papers are provided, if available.
Cite as

Knut Reinert, Christian Huber, Kathrin Marcus, Michal Linial, and Oliver Kohlbacher. 08101 Abstracts Collection – Computational Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 8101, pp. 1-34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{reinert_et_al:DagSemProc.08101.1,
  author =	{Reinert, Knut and Huber, Christian and Marcus, Kathrin and Linial, Michal and Kohlbacher, Oliver},
  title =	{{08101 Abstracts  Collection – Computational Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--34},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8101},
  editor =	{Christian Huber and Oliver Kohlbacher and Michal Linial and Katrin Marcus and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08101.1},
  URN =		{urn:nbn:de:0030-drops-17840},
  doi =		{10.4230/DagSemProc.08101.1},
  annote =	{Keywords: Bioinformatics, biomedicine, proteomics, analytical chemistry}
}
Document
DOI: 10.4230/DagSemProc.08101.2
Towards de novo identification of metabolites by analyzing tandem mass spectra

Authors: Sebastian Böcker and Florian Rasche

Abstract
Mass spectrometry is among the most widely used technologies in proteomics and metabolomics. For metabolites, de novo interpretation of spectra is even more important than for protein data, because metabolite spectra databases cover only a small fraction of naturally occurring metabolites. In this work, we analyze a method for fully automated de novo identification of metabolites from tandem mass spectra. Mass spectrometry data is usually assumed to be insufficient for identification of molecular structures, so we want to estimate the molecular formula of the unknown metabolite, a crucial step for its identification. This is achieved by calculating the possible formulas of the fragment peaks and then reconstructing the most likely fragmentation tree from this information. We present tests on real mass spectra showing that our algorithms solve the reconstruction problem suitably fast and provide excellent results: For all 32 test compounds the correct solution was among the top five suggestions, for 26 compounds the first suggestion of the exact algorithm was correct.
Cite as

Sebastian Böcker and Florian Rasche. Towards de novo identification of metabolites by analyzing tandem mass spectra. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 8101, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{bocker_et_al:DagSemProc.08101.2,
  author =	{B\"{o}cker, Sebastian and Rasche, Florian},
  title =	{{Towards de novo identification of metabolites by analyzing tandem mass spectra}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8101},
  editor =	{Christian Huber and Oliver Kohlbacher and Michal Linial and Katrin Marcus and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08101.2},
  URN =		{urn:nbn:de:0030-drops-17839},
  doi =		{10.4230/DagSemProc.08101.2},
  annote =	{Keywords: Tandem mass spectrometry, metabolomics, de novo interpretation}
}

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  • Authors
  • B
  • Böcker, Sebastian
  • H
  • Huber, Christian
  • K
  • Kohlbacher, Oliver
  • L
  • Linial, Michal
  • M
  • Marcus, Kathrin
  • R
  • Rasche, Florian
  • Reinert, Knut

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