xComb: A Cross-Linked Peptide Database Approach to Protein−Protein Interaction Analysis

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• 作者：Alexandre Panchaud ; Pragya Singh ; Scott A. Shaffer ; David R. Goodlett
• 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：2508-2515
• 全文大小：384K
• 年卷期：v.9,no.5(May 7, 2010)
• ISSN：1535-3907

文摘

We developed an informatic method to identify tandem mass spectra composed of chemically cross-linked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and X!Tandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community.