Inferring Peptide Composition from Molecular Formulas

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


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.


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.


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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

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