An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum

  • Bin Ma
  • Kaizhong Zhang
  • Chengzhi Liang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2676)


The determination of the amino acid sequence of a peptide from its MS/MS spectrum is an important task in proteomics. The determination without the help of a protein database is called the de novo sequencing, which is especially useful in the identification of unknown proteins. Many studies on the de novo sequencing problem have been done but none proves to be practical. In this paper, we define a new model for this problem, and provide a sophisticated dynamic programming algorithm to solve it. Experiments on real MS/MS data demonstrated that the algorithm works very well on QTof MS/MS data.


Peptide Sequencing Score Function Tandem Mass Spectrum Sequencing Problem Fast Atom Bombardment Mass Spectrometry 
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 2003

Authors and Affiliations

  • Bin Ma
    • 1
  • Kaizhong Zhang
    • 1
  • Chengzhi Liang
    • 2
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondonCanada
  2. 2.Bioinformatics Solutions Inc.WaterlooCanada

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