Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry

doi:10.16476/j.pibb.2021.0057

	Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry
	Chen Zhen-Lin 1,2; Cao Yong 3; He Si-Min 1,2
	2022-04-01
发表期刊	PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
ISSN	1000-3282
卷号	49 期号:4 页码:737-758
摘要	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.
关键词	cross-linking mass spectrometry protein structure protein interaction proteomics mass spectrometry
DOI	10.16476/j.pibb.2021.0057
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[32071435] ; National Basic Research Program of China[2016YFA0501300]
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
WOS类目	Biochemistry & Molecular Biology ; Biophysics
WOS记录号	WOS:000794195500011
出版者	CHINESE ACAD SCIENCES, INST BIOPHYSICS
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/19557
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	He Si-Min
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Natl Inst Biol Sci, Beijing 102206, Peoples R China
推荐引用方式 GB/T 7714	Chen Zhen-Lin,Cao Yong,He Si-Min. Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry[J]. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,2022,49(4):737-758.
APA	Chen Zhen-Lin,Cao Yong,&He Si-Min.(2022).Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry.PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS,49(4),737-758.
MLA	Chen Zhen-Lin,et al."Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry".PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 49.4(2022):737-758.