化学交联质谱技术的研究进展

化学交联质谱技术是解析蛋白质结构和研究蛋白质相互作用的重要工具。近5年以来，该技术在方法和应用上都取得了很大的进步。方法上，一方面可断裂交联剂与新型分离富集方法展现了较好的应用前景，另一方面更加高效的交联肽段搜索引擎和质量控制方法为交联质谱数据分析提供了有力的工具。应用上，一方面与冷冻电镜技术结合解析了大量蛋白质的结构，另一方面从研究蛋白质复合物的相互作用发展到研究全蛋白质组水平的相互作用网络。化学交联质谱技术在方法和应用上的蓬勃发展，体现了这一技术的重要作用。本文对化学交联质谱技术的各个环节进行了详细的综述，包括交联剂选择、交联反应、酶切、交联肽段富集、液质联用、交联肽段鉴定、质量控制和生物学应用，重点介绍了最近5年的研究进展。最后，讨论了化学交联质谱技术面临的挑战及未来的发展方向。

Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry

Chemical cross-linking coupled with mass spectrometry (CXMS) is an important tool to analyze protein structures and protein-protein interactions. In the last five years, CXMS has made great progress in both methods and applications. In terms of methods, on the one hand, cleavable cross-linkers and new separation and enrichment methods have shown good prospects, and on the other hand, more efficient cross-linked peptide search engines and quality control methods provide powerful tools for CXMS data analysis. In terms of applications, on the one hand, CXMS combined with cryo-electron microscopy has determined a large number of protein structures, and on the other hand, CXMS has shown the potential to analyze protein-protein interaction networks at a proteome scale. The intensive research on CXMS in methods and applications reflect the important role of this technology. Here we review the various aspects of CXMS, including cross-linker selection, cross-linking reaction, protein digestion, separation and enrichment, data acquisition, cross-linked peptide identification, quality control, and application, and mainly focus on progress in the last five years. Lastly, we discuss the challenges and opportunities of CXMS in the future. In section 1, we review cross-linkers from the aspects of reactive group and spacer arm. In section 2, we give tips for the cross-linking reaction. In section 3, we describe the sequential digestion strategy for cross-linked proteins. In section 4, we elaborate enrichment methods for cross-linked peptides, including affinity purification, chromatographic separation, and ion mobility mass spectrometry. In section 5, we elaborate data acquisition methods for cross-linked peptides, and compare three methods for MS-cleavable cross-linked peptides. In section 6, we elaborate search engines for cross-linked peptide identification. In section 7, we describe quality control methods for cross-linked peptide identification. In section 8, we review applications of CXMS and list some proteome-wide CXMS studies. In section 9, we conclude the paper and discuss the challenges and opportunities of CXMS in the future.