Abstract
Mass spectrometry is one of the key technologies in metabolomics for the identification and quantification of molecules in small concentrations. For identification, these molecules are fragmented by, e.g., tandem mass spectrometry, and masses and abundances of the resulting fragments are measured. Recently, methods for de novo interpretation of tandem mass spectra and the automated inference of fragmentation patterns have been developed. If the correct structural formula is known, then peaks in the fragmentation pattern can be annotated by substructures of the underlying compound. To determine the structure of these fragments manually is tedious and time-consuming. Hence, there is a need for automated identification of the generated fragments.
In this work, we consider the problem of annotating fragmentation patterns. Our input are fragmentation trees, representing tandem mass spectra where each peak has been assigned a molecular formula, and fragmentation dependencies are known. Given a fixed structural formula and any fragment molecular formula, we search for all structural fragments that satisfy elemental multiplicities. Ultimately, we search for a fragmentation pattern annotation with minimum total cleavage costs. We discuss several algorithmic approaches for this problem, including a randomized and a tree decomposition-based algorithm. We find that even though the problem of identifying structural fragments is NP-hard, instances based on molecular structures can be efficiently solved with a classical branch-and-bound algorithm.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alon, N., Yuster, R., Zwick, U.: Color-coding. J. ACM 42(2), 844–856 (1995)
Betzler, N., Fellows, M.R., Komusiewicz, C., Niedermeier, R.: Parameterized algorithms and hardness results for some graph motif problems. In: Ferragina, P., Landau, G.M. (eds.) CPM 2008. LNCS, vol. 5029, pp. 31–43. Springer, Heidelberg (2008)
Böcker, S., Letzel, M., Lipták, Z., Pervukhin, A.: SIRIUS: Decomposing isotope patterns for metabolite identification. Bioinformatics 25(2), 218–224 (2009)
Böcker, S., Rasche, F.: Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics 24, I49–I55 (2008); Proc. of European Conference on Computational Biology (ECCB 2008)
Böcker, S., Zichner, T., Rasche, F.: Automated classification of unknown biocompounds using tandem MS. In: Poster Proc. of Conference of the American Society for Mass Spectrometry (ASMS 2009), p. W690 (2009)
Cai, L., Chan, S.M., Chan, S.O.: Random separation: a new method for solving fixed-cardinality optimization problems. In: Bodlaender, H.L., Langston, M.A. (eds.) IWPEC 2006. LNCS, vol. 4169, pp. 239–250. Springer, Heidelberg (2006)
Fellows, M., Fertin, G., Hermelin, D., Vialette, S.: Sharp tractability borderlines for finding connected motifs in vertex-colored graphs. In: Arge, L., Cachin, C., Jurdziński, T., Tarlecki, A. (eds.) ICALP 2007. LNCS, vol. 4596, pp. 340–351. Springer, Heidelberg (2007)
Fernie, A.R., Trethewey, R.N., Krotzky, A.J., Willmitzer, L.: Metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell Biol. 5(9), 763–769 (2004)
Heinonen, M., Rantanen, A., Mielikäinen, T., Kokkonen, J., Kiuru, J., Ketola, R.A., Rousu, J.: FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun. Mass Spectrom. 22(19), 3043–3052 (2008)
Kloks, T.: Treewidth, Computation and Approximation. Springer, Heidelberg (1994)
Niedermeier, R.: Invitation to Fixed-Parameter Algorithms. Oxford University Press, Oxford (2006)
Rogers, S., Scheltema, R.A., Girolami, M., Breitling, R.: Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics 25(4), 512–518 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Böcker, S., Rasche, F., Steijger, T. (2009). Annotating Fragmentation Patterns. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_2
Download citation
DOI: https://doi.org/10.1007/978-3-642-04241-6_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04240-9
Online ISBN: 978-3-642-04241-6
eBook Packages: Computer ScienceComputer Science (R0)