ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database.
ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database.
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ECL：使用整个数据库识别交联肽的详尽搜索工具
DOI：
10.1186/s12859-016-1073-y
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发表时间：
2016-05-20
影响因子：
3
通讯作者：
Yu W
中科院分区：
文献类型：
--
作者：
Yu F;Li N;Yu W
背景化学交联结合质谱（CX-MS）是研究蛋白质相互作用的一种高通量方法。肽-肽组合的数量相对于蛋白质的数量呈二次方增长，导致高计算复杂性。广泛使用的方法包括xQuest（Rinner等人，Nat Methods 5（4）：315-8，2008; Walzthoeni等人，Nat Methods 9（9）：901-3，2012）、pLink（Yang等人，Nat Methods 9（9）：904-6，2012）、ProteinProspector（Chu等人，Mol Cell Proteomics 9：25-31，2010; Trnka等人，13（2）：420-34，2014）和Kojak（Hoopmann等人，J Proteome Res 14（5）：2190-198，2015）通过用启发式方法预先选择肽来避免搜索所有肽-肽组合。然而，预选程序可能会造成调查结果缺失。最直观的方法是搜索所有可能的候选人。因此，一个工具，可以彻底搜索整个数据库，没有任何启发式的预选程序是可取的。ResultsWe已经开发出一种交联肽识别工具，名为ECL。它可以在合理的时间内对整个数据库进行穷举搜索，而不需要任何启发式的预选过程。测试表明，搜索包含5200个蛋白质的数据库需要7小时。ECL确定了更多的非冗余交联肽比xQuest，pLink和ProteinProspector。实验表明，这些额外鉴定的肽中约30%未被Kojak预先选择。我们使用来自蛋白质数据库的蛋白质晶体结构来检查蛋白质内交联肽。大多数交联位点之间的距离小于30 μ m。结论据我们所知，ECL是第一个可以彻底搜索所有候选交联肽鉴定的工具。实验表明，ECL比xQuest、pLink和ProteinProspector能识别更多的肽段。进一步的分析表明，一些额外的识别结果是由于详尽的搜索。
BackgroundChemical cross-linking combined with mass spectrometry (CX-MS) is a high-throughput approach to studying protein-protein interactions. The number of peptide-peptide combinations grows quadratically with respect to the number of proteins, resulting in a high computational complexity. Widely used methods including xQuest (Rinner et al., Nat Methods 5(4):315–8, 2008; Walzthoeni et al., Nat Methods 9(9):901–3, 2012), pLink (Yang et al., Nat Methods 9(9):904–6, 2012), ProteinProspector (Chu et al., Mol Cell Proteomics 9:25–31, 2010; Trnka et al., 13(2):420–34, 2014) and Kojak (Hoopmann et al., J Proteome Res 14(5):2190–198, 2015) avoid searching all peptide-peptide combinations by pre-selecting peptides with heuristic approaches. However, pre-selection procedures may cause missing findings. The most intuitive approach is searching all possible candidates. A tool that can exhaustively search a whole database without any heuristic pre-selection procedure is therefore desirable.ResultsWe have developed a cross-linked peptides identification tool named ECL. It can exhaustively search a whole database in a reasonable period of time without any heuristic pre-selection procedure. Tests showed that searching a database containing 5200 proteins took 7 h.ECL identified more non-redundant cross-linked peptides than xQuest, pLink, and ProteinProspector. Experiments showed that about 30%of these additional identified peptides were not pre-selected by Kojak. We used protein crystal structures from the protein data bank to check the intra-protein cross-linked peptides. Most of the distances between cross-linking sites were smaller than 30 Å.ConclusionsTo the best of our knowledge, ECL is the first tool that can exhaustively search all candidates in cross-linked peptides identification. The experiments showed that ECL could identify more peptides than xQuest, pLink, and ProteinProspector. A further analysis indicated that some of the additional identified results were thanks to the exhaustive search.