Probabilistic De Novo Peptide Sequencing with Doubly Charged Ions

  • Hansruedi Peter
  • Bernd Fischer
  • Joachim M. Buhmann
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4174)


Sequencing of peptides by tandem mass spectrometry has matured to the key technology for proteomics. Noise in the measurement process strongly favors statistical models like NovoHMM, a recently published generative approach based on factorial hidden Markov models [1,2]. We extend this hidden Markov model to include information of doubly charged ions since the original model can only cope with singly charged ions. This modification requires a refined discretization of the mass scale and, thereby, it increases its sensitivity and recall performance on a number of datasets to compare favorably with alternative approaches for mass spectra interpretation.


Hide Markov Model Tandem Mass Spectrometry Markov Chain Model Emission Variable Correct Amino Acid 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Hansruedi Peter
    • 1
  • Bernd Fischer
    • 1
  • Joachim M. Buhmann
    • 1
  1. 1.Institute of Computational ScienceETH ZurichSwitzerland

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