For the identification of peptides with
tandem mass spectrometry (MS/MS), many software tools rely on the comparison between an experimental spectrum and a theoretically predicted spectrum. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the peptide identification performance and is an impor
tant problem for mass spectrometry based proteomics. In this study a new approach, called MS-Simulator, is presented for predicting the
y-ion intensities in the spectrum of a given peptide. The new approach focuses on the accurate prediction of the relative intensity ratio between every two adjacent
y-ions. The theoretical spectrum can then be derived from these ratios. The prediction of a ratio is a closed-form equation that involves up to five consecutive amino acids nearby the two
y-ions and the two peptide termini. Compared with another existing spectrum prediction tool MassAnalyzer, the new approach not only simplifies the computation, but also improves the prediction accuracy.
Keywords:
mass spectrometry; spectrum prediction; mobile proton hypothesis; peptide identification