Rapid generation of peptide sequence tags with a graph search algorithm

Tandem mass spectrometry is a popular tool for the identification of peptide sequences. In this paper, we present a method for rapid generation of short peptide sequences via tandem mass spectrometry based on a graph search. 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 find 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 PepNovo approaches with higher efficiency.