A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry

Details A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry

2001-01-18

arxiv.org/abs/cs/0101016v1

Computer Science

Computational Engineering, Finance, and Science

A preliminary version appeared in Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 389--398, 20

Scientific paper

The tandem mass spectrometry fragments a large number of molecules of the same peptide sequence into charged prefix and suffix subsequences, and then measures mass/charge ratios of these ions. The de novo peptide sequencing problem is to reconstruct the peptide sequence from a given tandem mass spectral data of k ions. By implicitly transforming the spectral data into an NC-spectrum graph G=(V,E) where |V|=2k+2, we can solve this problem in O(|V|+|E|) time and O(|V|) space using dynamic programming. Our approach can be further used to discover a modified amino acid in O(|V||E|) time and to analyze data with other types of noise in O(|V||E|) time. Our algorithms have been implemented and tested on actual experimental data.

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