Detecting Cross-Linked Peptides by Searching against a Database of Cross-Linked Peptide Pairs

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• 作者：Sean McIlwain ; Paul Draghicescu ; Pragya Singh ; David R. Goodlett ; William Stafford Noble
• 刊名：Journal of Proteome Research
• 出版年：2010
• 出版时间：May 7, 2010
• 年：2010
• 卷：9
• 期：5
• 页码：2488-2495
• 全文大小：258K
• 年卷期：v.9,no.5(May 7, 2010)
• ISSN：1535-3907

文摘

Mass spectrometric identification of cross-linked peptides can provide valuable information about the structure of protein complexes. We describe a straightforward database search scheme that identifies and assigns statistical confidence estimates to spectra from cross-linked peptides. The method is well suited to targeted analysis of a single protein complex, without requiring an isotope labeling strategy. Our approach uses a SEQUEST-style search procedure in which the database is comprised of a mixture of single peptides with and without linkers attached and cross-linked products. In contrast to several previous approaches, we generate theoretical spectra that account for all of the expected peaks from a cross-linked product, and we employ an empirical curve-fitting procedure to estimate statistical confidence measures. We show that our fully automated procedure successfully reidentifies spectra from a previous study, and we provide evidence that our statistical confidence estimates are accurate.