Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China.
University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China.
J Am Soc Mass Spectrom. 2021 Sep 1;32(9):2410-2416. doi: 10.1021/jasms.1c00120. Epub 2021 Jul 28.
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 ()) 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 cell lysate cross-linked by a newly synthesized enrichable cross-linker, pDSBE. The approach can be applicable to both cleavable and noncleavable methods.
交联质谱方法由于计算复杂度（O()）问题，尚未成功应用于全蛋白质组水平的蛋白质-蛋白质相互作用发现。在之前的一份报告中，我们提出了一种决策树搜索策略（DTSS），可以将复杂度降低几个数量级。在本研究中，我们进一步发现单连接肽携带了相应交联对保留时间的信息；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筛选器，假阳性率可以降低约 86%，而敏感性损失 10%。结合 DTSS 的方法（T-DTSS）不仅有利于提高鉴定置信度，而且可以降低截止分数，并大大促进交联内鉴定。T-DTSS 成功应用于从新合成的可富集交联剂 pDSBE 交联的细胞裂解物中获得的交联内鉴定。该方法可适用于可切割和不可切割的方法。
