Xilmass: A New Approach toward the Identification of Cross-Linked Peptides.
Xilmass: A New Approach toward the Identification of Cross-Linked Peptides.
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Xilmass：鉴定交联肽的新方法
DOI：
10.1021/acs.analchem.6b01585
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发表时间：
2016
影响因子：
7.4
通讯作者：
Vandermarliere E
中科院分区：
文献类型：
--
作者：
Yılmaz Su;Drepper F;Hulstaert N;Černič Ma;Gevaert K;Economou A;Warscheid B;Martens L;Vandermarliere E
化学交联与质谱联用在揭示蛋白质相互作用，特别是微弱和短暂的相互作用方面起着重要作用。此外，交联补充了几种结构测定方法，如cryo-EM。虽然有几种计算方法可用于从交联肽获得的光谱的注释，但仍有改进的空间。在这里，我们提出了Xilmass，一种识别交联肽的新算法，引入了两个新概念：（i）在搜索数据库中表示交联肽，使得交联位点被明确编码，和（ii）从Andromeda算法导出的评分函数适于针对理论串联质谱（MS/MS）进行评分包含来自交联肽对的所有可能碎片离子的峰的光谱。针对最近发表的Kojak和流行的pLink算法，在钙调蛋白-凝集素复合物数据集以及另外三个已发表的数据集上评估了Xilmass的性能。结果表明，Xilmass通常具有最高数量的鉴定的不同交联位点，也具有最高数量的预测交联位点。
Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient ones. Moreover, cross-linking complements several structural determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in the search database such that the cross-linking sites are explicitly encoded, and (ii) the scoring function derived from the Andromeda algorithm was adapted to score against a theoretical tandem mass spectrometry (MS/MS) spectrum that contains the peaks from all possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was evaluated against the recently published Kojak and the popular pLink algorithms on a calmodulin-plectin complex data set, as well as three additional, published data sets. The results show that Xilmass typically had the highest number of identified distinct cross-linked sites and also the highest number of predicted cross-linked sites.
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