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Bioinformatics Advance Access originally published online on November 17, 2008
Bioinformatics 2009 25(2):218-224; doi:10.1093/bioinformatics/btn603
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SIRIUS: decomposing isotope patterns for metabolite identification{dagger}

Sebastian Böcker 1, Matthias C. Letzel 2, Zsuzsanna Lipták 3 and Anton Pervukhin 1,*

1Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, 07743 Jena, 2Organische Chemie I, Fakultät für Chemie, Universität Bielefeld, 33501 Bielefeld and 3AG Genominformatik, Technische Fakultät, Universität Bielefeld, 33501 Bielefeld, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: High-resolution mass spectrometry (MS) is among the most widely used technologies in metabolomics. Metabolites participate in almost all cellular processes, but most metabolites still remain uncharacterized. Determination of the sum formula is a crucial step in the identification of an unknown metabolite, as it reduces its possible structures to a hopefully manageable set.

Results: We present a method for determining the sum formula of a metabolite solely from its mass and the natural distribution of its isotopes. Our input is a measured isotope pattern from a high resolution mass spectrometer, and we want to find those molecules that best match this pattern. Our method is computationally efficient, and results on experimental data are very promising: for orthogonal time-of-flight mass spectrometry, we correctly identify sum formulas for >90% of the molecules, ranging in mass up to 1000 Da.

Availability: SIRIUS is available under the LGPL license at http://bio.informatik.uni-jena.de/sirius/

Contact: anton.pervukhin{at}minet.uni-jena.de

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}Apreliminary version of this article appeared under the title ‘Decomposing metabolomic isotope patterns’ in the Proceedings of the 6th Workshop on Algorithms in Bioinformatics, WABI 2006, in LNCS, Vol. 4175, Springer, pp. 12–23.

Associate Editor: Olga Troyanskaya

Received on August 28, 2008; revised on November 13, 2008; accepted on November 14, 2008

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