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Accurate Retention Time Prediction Based on Monolinked Peptide Information to Confidently Identify Cross-Linked Peptides.
Journal of the American Society for Mass Spectrometry ( IF 3.2 ) Pub Date : 2021-07-28 , DOI: 10.1021/jasms.1c00120
Rong Huang 1, 2 , Wei Zhu 1 , Zili Xu 1 , Jiakang Chen 1 , Biao Jiang 1 , Hongli Chen 1 , Wenzhang Chen 1
Affiliation  

Cross-linking mass spectrometry methods have not been successfully applied to protein-protein interaction discovery at a proteome-wide level mainly due to the computation complexity (O (n2)) issue. In a previous report, we proposed a decision tree searching strategy (DTSS), which can reduce complexity by orders of magnitude. In this study, we further found that the monolinked peptides carry out the information on the retention time of the corresponding cross-linked pairs; therefore, the retention time of cross-linked peptide pairs can be predicted accurately. By utilizing the retention time as an extra filter, the false positive rate can be reduced by around 86% with a sensitivity loss of 10%. The method combined with DTSS (T-DTSS) not only benefits improving identification confidence but also leads to lower cutoff scores and facilitates substantially increasing inter-cross-link identification. T-DTSS was successfully applied to the identification of inter-cross-links obtained from Escherichia coli cell lysate cross-linked by a newly synthesized enrichable cross-linker, pDSBE. The approach can be applicable to both cleavable and noncleavable methods.

中文翻译:

基于单链肽信息的准确保留时间预测,以可靠地识别交联肽。

主要由于计算复杂性 (O (n2)) 问题,交联质谱方法尚未成功应用于蛋白质组范围内的蛋白质-蛋白质相互作用发现。在之前的报告中,我们提出了一种决策树搜索策略(DTSS),可以将复杂性降低几个数量级。在这项研究中,我们进一步发现单联肽执行了有关相应交联对的保留时间的信息;因此,可以准确预测交联肽对的保留时间。通过利用保留时间作为额外的过滤器,可以将假阳性率降低约 86%,灵敏度损失 10%。该方法与 DTSS (T-DTSS) 相结合不仅有利于提高识别置信度,而且还可以降低截止分数,并有助于显着提高跨链接识别。T-DTSS 已成功应用于鉴定通过新合成的可富集交联剂 pDSBE 交联的大肠杆菌细胞裂解液中的交联。该方法可以适用于可切割和不可切割的方法。
更新日期:2021-07-28
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