An effective algorithm for the peptide de novo sequencing from MS/MS spectrum

Authors:
Bin Ma;Kaizhong Zhang;Chengzhi Liang
Affiliations:
Department of Computer Science, University of Western Ontario, London, ON, Canada;Department of Computer Science, University of Western Ontario, London, ON, Canada;Bioinformatics Solutions Inc., Waterloo, ON, Canada
Venue:
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Year:
2003

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Abstract

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.