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MS-Simulator: Predicting Y‑Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

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posted on 07.09.2012, 00:00 by Shiwei Sun, Fuquan Yang, Qing Yang, Hong Zhang, Yaojun Wang, Dongbo Bu, Bin Ma
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 important 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.

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