MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions
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- 作者：Shiwei Sun ; Fuquan Yang ; Qing Yang ; Hong Zhang ; Yaojun Wang ; Dongbo Bu ; Bin Ma
- 刊名：Journal of Proteome Research
- 出版年：2012
- 出版时间：September 7, 2012
- 年：2012
- 卷：11
- 期：9
- 页码：4509-4516
- 全文大小：355K
- 年卷期：v.11,no.9(September 7, 2012)
- ISSN：1535-3907
文摘
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.