Advertisement

Inferring Peptide Composition from Molecular Formulas

  • Sebastian Böcker
  • Anton Pervukhin
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5609)

Abstract

With the advent of novel mass spectrometry techniques such as Orbitrap MS, it is possible to determine the exact molecular formula of an unknown molecule solely from its isotope pattern. But for protein mass spectrometry, one is facing the problem that many peptides have exactly the same molecular formula even when ignoring the order of amino acids. In this work, we present an efficient method to determine the amino acid composition of an unknown peptide solely from its molecular formula. Our solution is based on efficiently enumerating all solutions of the multi-dimensional equality constrained integer knapsack problem.

Keywords

Amino Acid Composition Molecular Formula Competitive Ratio Decomposition Algorithm Gaussian Elimination 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Aardal, K., Lenstra, A.K.: Hard equality constrained integer knapsacks. In: Cook, W.J., Schulz, A.S. (eds.) IPCO 2002. LNCS, vol. 2337, pp. 350–366. Springer, Heidelberg (2002)Google Scholar
  2. 2.
    Bandeira, N., Ng, J., Meluzzi, D., Linington, R.G., Dorrestein, P., Pevzner, P.A.: De novo sequencing of nonribosomal peptides. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 181–195. Springer, Heidelberg (2008)Google Scholar
  3. 3.
    Beck, M., Gessel, I.M., Komatsu, T.: The polynomial part of a restricted partition function related to the Frobenius problem. Electron. J. Comb. 8(1), N7 (2001)Google Scholar
  4. 4.
    Böcker, S., Letzel, M., Lipták, Z., Pervukhin, A.: Decomposing metabolomic isotope patterns. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 12–23. Springer, Heidelberg (2006)Google Scholar
  5. 5.
    Böcker, S., Letzel, M., Lipták, Z., Pervukhin, A.: SIRIUS: Decomposing isotope patterns for metabolite identification. Bioinformatics 25(2), 218–224 (2009)CrossRefGoogle Scholar
  6. 6.
    Böcker, S., Lipták, Z.: A fast and simple algorithm for the Money Changing Problem. Algorithmica 48(4), 413–432 (2007)MathSciNetCrossRefzbMATHGoogle Scholar
  7. 7.
    Fürst, A., Clerc, J.-T., Pretsch, E.: A computer program for the computation of the molecular formula. Chemom. Intell. Lab. Syst. 5, 329–334 (1989)CrossRefGoogle Scholar
  8. 8.
    Haas, W., Faherty, B.K., Gerber, S.A., Elias, J.E., Beausoleil, S.A., Bakalarski, C.E., Li, X., Ville, J., Gygi, S.P.: Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol. Cell. Proteomics 5(7), 1326–1337 (2006)CrossRefGoogle Scholar
  9. 9.
    He, F., Hendrickson, C.L., Marshall, A.G.: Baseline mass resolution of peptide isobars: A record for molecular mass resolution. Anal. Chem. 73(3), 647–650 (2001)CrossRefGoogle Scholar
  10. 10.
    Olsen, J.V., de Godoy, L.M.F., Li, G., Macek, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S., Mann, M.: Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a c-trap. Mol. Cell. Proteomics 4, 2010–2021 (2006)CrossRefGoogle Scholar
  11. 11.
    Papp, D., Vizvári, B.: Effective solution of linear diophantine equation systems with an application in chemistry. J. Math. Chem. 39(1), 15–31 (2006)MathSciNetCrossRefzbMATHGoogle Scholar
  12. 12.
    Rockwood, A.L., Van Orden, S.L.: Ultrahigh-speed calculation of isotope distributions. Anal. Chem. 68, 2027–2030 (1996)CrossRefGoogle Scholar
  13. 13.
    Tanner, S., Payne, S.H., Dasari, S., Shen, Z., Wilmarth, P.A., David, L.L., Loomis, W.F., Briggs, S.P., Bafna, V.: Accurate annotation of peptide modifications through unrestrictive database search. J. Proteome Res. 7, 170–181 (2008)CrossRefGoogle Scholar
  14. 14.
    von Roepenack-Lahaye, E., Degenkolb, T., Zerjeski, M., Franz, M., Roth, U., Wessjohann, L., Schmidt, J., Scheel, D., Clemens, S.: Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol. 134(2), 548–559 (2004)CrossRefGoogle Scholar
  15. 15.
    Wilf, H.: Generating functionology, 2nd edn. Academic Press, London (1994)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Sebastian Böcker
    • 1
    • 2
  • Anton Pervukhin
    • 1
  1. 1.Institut für InformatikFriedrich-Schiller-Universität JenaGermany
  2. 2.Jena Centre for BioinformaticsJenaGermany

Personalised recommendations