Optimal Transitions for Targeted Protein Quantification: Best Conditioned Submatrix Selection

  • Rastislav Šrámek
  • Bernd Fischer
  • Elias Vicari
  • Peter Widmayer
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5609)


Multiple reaction monitoring (MRM) is a mass spectrometric method to quantify a specified set of proteins. In this paper, we identify a problem at the core of MRM peptide quantification accuracy. In mathematical terms, the problem is to find for a given matrix a submatrix with best condition number. We show this problem to be NP-hard, and we propose a greedy heuristic. Our numerical experiments show this heuristic to be orders of magnitude better than currently used methods.


bioinformatics submatrix selection problem minimal condition number 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Rastislav Šrámek
    • 1
  • Bernd Fischer
    • 2
  • Elias Vicari
    • 1
  • Peter Widmayer
    • 1
  1. 1.Department of Computer ScienceETH ZurichZurichSwitzerland
  2. 2.European Bioinformatics InstituteCambridgeUnited Kingdom

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