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Determination of Glycan Structure from Tandem Mass Spectra

  • Sebastian Böcker
  • Birte Kehr
  • Florian Rasche
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5609)

Abstract

Glycans are molecules made from simple sugars that form complex tree structures. Glycans constitute one of the most important protein modifications, and identification of glycans remains a pressing problem in biology. Unfortunately, the structure of glycans is hard to predict from the genome sequence of an organism.

We consider the problem of deriving the topology of a glycan solely from tandem mass spectrometry data. We want to generate glycan tree candidates that sufficiently match the sample mass spectrum. Unfortunately, the resulting problem is known to be computationally hard. We present an efficient exact algorithm for this problem based on fixed-parameter algorithmics, that can process a spectrum in a matter of seconds. We also report some preliminary results of our method on experimental data. We show that our approach is fast enough in applications, and that we can reach very good de novo identification results. Finally, we show how to compute the number of glycan topologies of a given size.

Keywords

Tandem Mass Spectrum Full Paper Sample Spectrum Glycan Structure Parent Mass 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Sebastian Böcker
    • 1
    • 2
  • Birte Kehr
    • 1
  • Florian Rasche
    • 1
  1. 1.Lehrstuhl für BioinformatikFriedrich-Schiller-Universität JenaJenaGermany
  2. 2.Jena Centre for BioinformaticsJenaGermany

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