xComb: a cross-linked peptide database approach to protein-protein interaction analysis.
xComb: a cross-linked peptide database approach to protein-protein interaction analysis.
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DOI：
10.1021/pr9011816
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发表时间：
2010-05-07
影响因子：
4.4
通讯作者：
Goodlett, David R.
中科院分区：
文献类型：
--
作者：
Panchaud, Alexandre;Singh, Pragya;Shaffer, Scott A.;Goodlett, David R.
我们开发了一种信息学方法来识别由化学交联肽和线性肽组成的串联质谱，并为每两个独特的肽序列分配序列。对于给定的一组蛋白质，关键的软件工具xComb会梳理所有理论上可行的交联肽，以创建一个数据库，该数据库由所有组合的子集组成，表示为肽FASTA文件。xComb选择的理论交联肽库可以用作标准蛋白质组学搜索引擎检查的数据库，以匹配串联质谱数据集以识别交联肽。使用一些常用的蛋白质组学搜索引擎（如Phenyx、Sequest、OMSSA、Mascot和X!），可以对多达50种蛋白质进行数据库搜索。串联。通过对线性化交联肽的肽库进行搜索，而不是对线性化蛋白质库进行搜索，减少了搜索时间，并且该过程与任何特定的搜索引擎解耦。与搜索引擎脱钩的另一个好处是，蛋白质交联研究可以使用现成的信息学工具进行，这些工具在蛋白质组学社区中已经存在评分例程。
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 datasets 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.
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