Title: Peptide sequence tag generation for tandem mass spectra containing post-translational modifications

Authors: Hui Li; Chunmei Liu

Addresses: Department of Systems and Computer Science, Howard University, 2300 Sixth Street, NW, Washington, DC 20059, USA. ' Department of Systems and Computer Science, Howard University, 2300 Sixth Street, NW, Washington, DC 20059, USA

Abstract: Tandem mass spectrometry is a popular tool for the identification of peptide sequences. In this paper, we present a method for a rapid generation of short peptide sequences via tandem mass spectrometry based on a graph search method. The approach takes advantage of several pairs of peaks that have high intensities. We proposed a Pair Peak value Set (PPS) and used the pair peak values of highest intensities as the root of a tree. The other nodes are viewed as the reference nodes to search the most promising path. We aimed to determine the peptide sequences for MS/MS spectra that have low signal-to-noise ratios. Our experiment on 2420 experimental MS/MS spectra with two PTMs shows that our algorithm achieves better accuracy than the PepNovo approach with higher efficiency.

Keywords: tandem mass spectrum; PTM; post-translational modification; peptide sequence tags; sequence tag generation; peptide sequences; tandem mass spectrometry; graph search.

DOI: 10.1504/IJCBDD.2012.049209

International Journal of Computational Biology and Drug Design, 2012 Vol.5 No.3/4, pp.325 - 334

Published online: 05 Dec 2014 *

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