Swammerdam Institute for Life Sciences, Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 HX Amsterdam, the Netherlands.
Swammerdam Institute for Life Sciences, Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 HX Amsterdam, the Netherlands.
Biochim Biophys Acta Proteins Proteom. 2021 Jul;1869(7):140655. doi: 10.1016/j.bbapap.2021.140655. Epub 2021 Mar 31.
Chemical cross-linking (CX) of proteins in vivo or in cell free extracts followed by mass spectrometric (MS) identification of linked peptide pairs (CXMS) can reveal protein-protein interactions (PPIs) both at a proteome wide scale and the level of cross-linked amino acid residues. However, error estimation at the level of PPI remains challenging in large scale datasets. Here we discuss recent advances in the recognition of spurious inter-protein peptide pairs and in diminishing the FDR for these PPI-signaling cross-links, such as the use of chromatographic retention time prediction, in order to come to a more reliable reporting of PPIs.
化学交联（CX）的蛋白质在体内或无细胞提取物后，通过质谱（MS）鉴定的连接肽对（CXMS）可以揭示蛋白质-蛋白质相互作用（PPIs），无论是在蛋白质组学范围内还是交联氨基酸残基水平。然而，在大规模数据集的 PPI 水平上进行误差估计仍然具有挑战性。在这里，我们讨论了在识别虚假的蛋白质间肽对方面的最新进展，以及减少这些 PPI 信号交联的 FDR 的方法，例如使用色谱保留时间预测，以便更可靠地报告 PPIs。
