Database Search Algorithm for Identification of Intact Cross-Links in Proteins and Peptides Using Tandem Mass Spectrometry

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• 作者：Hua Xu ; Pang-Hung Hsu ; Liwen Zhang ; Ming-Daw Tsai ; Michael A. Freitas
• 刊名：Journal of Proteome Research
• 出版年：2010
• 出版时间：July 2, 2010
• 年：2010
• 卷：9
• 期：7
• 页码：3384-3393
• 全文大小：491K
• 年卷期：v.9,no.7(July 2, 2010)
• ISSN：1535-3907

文摘

A new database search algorithm has been developed for identification of intact cross-links in proteins and peptides from tandem mass spectrometric data. Using this algorithm, intact cross-links can be identified and characterized in proteins and peptides with high confidence. The algorithm was tested using BS³ (bis[sulfosuccinimidyl] suberate) cross-linked Cytochrome C. Five cross-links were identified and verified for spatial plausibility by comparison with its three-dimensional structure at optimized experimental conditions. The distributions of statistical scores for true and false positives and receiver operating characteristic analysis indicate that the algorithm is capable of discriminating true positive cross-linked peptide-spectrum matches from false ones. It has also been demonstrated that the MassMatrix database search engine is capable of searching for intact cross-links in complex Escherichia coli proteome samples cross-linked by BS³. The new algorithm in MassMatrix offers an additional approach for the discovery of cross-links in proteins and peptides from tandem mass spectrometric data.

Keywords:

chemical cross-link; tandem mass spectrometry; database search; proteomics