Peptide sequence tag generation for tandem mass spectra containing post-translational modifications
by Hui Li; Chunmei Liu
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 5, No. 3/4, 2012

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.

Online publication date: Fri, 05-Dec-2014

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