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.
@article{arxiv.cs/0101016,
title = {A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry},
author = {Ting Chen and Ming-Yang Kao and Matthew Tepel and John Rush and George M. Church},
journal= {arXiv preprint arXiv:cs/0101016},
year = {2007}
}
Comments
A preliminary version appeared in Proceedings of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 389--398, 2000