Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers

doi:10.1021/acs.jproteome.3c00037

	Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers
	Cao, Yong 1; Liu, Xin-Tong 1; Mao, Peng-Zhi 2,3; Chen, Zhen-Lin 2,3; Tarn, Ching 2,3; Dong, Meng-Qiu 1,4
	2023-07-26
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	22 期号:8 页码:2593-2607
摘要	When it comes to mass spectrometry data analysis foridentificationof peptide pairs linked by N-hydroxysuccinimide (NHS)ester cross-linkers, search engines bifurcate in their setting ofcross-linkable sites. Some restrict NHS ester cross-linkable sitesto lysine (K) and protein N-terminus, referred to as K only for short,whereas others additionally include serine (S), threonine (T), andtyrosine (Y) by default. Here, by setting amino acids with chemicallyinert side chains such as glycine (G), valine (V), and leucine (L)as cross-linkable sites, which serves as a negative control, we showthat software-identified STY-cross-links are only as reliable as GVL-cross-links.This is true across different NHS ester cross-linkers including DSS,DSSO, and DSBU, and across different search engines including MeroX,xiSearch, and pLink. Using a published data set originated from syntheticpeptides, we demonstrate that STY-cross-links indeed have a high falsediscovery rate. Further analysis revealed that depending on the dataand the search engine used to analyze the data, up to 65% of the STY-cross-linksidentified are actually K-K cross-links of the same peptidepairs, up to 61% are actually K-mono-links, and the rest tend to containshort peptides at high risk of false identification.
关键词	CXMS XL-MS NHS ester cross-linker pLink xiSearch MeroX
DOI	10.1021/acs.jproteome.3c00037
收录类别	SCI
语种	英语
资助项目	Ministry of Science and Technology of China[2020YFF01014505] ; municipal government of Beijing ; TIMBR ; Tsinghua University
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:001036853500001
出版者	AMER CHEMICAL SOC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/21298
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Cao, Yong; Dong, Meng-Qiu
作者单位	1.Natl Inst Biol Sci, Beijing 102206, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc Chinese Acad Sci, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Tsinghua Univ, Tsinghua Inst Multidisciplinary Biomed Res, Beijing 102206, Afghanistan
推荐引用方式 GB/T 7714	Cao, Yong,Liu, Xin-Tong,Mao, Peng-Zhi,et al. Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers[J]. JOURNAL OF PROTEOME RESEARCH,2023,22(8):2593-2607.
APA	Cao, Yong,Liu, Xin-Tong,Mao, Peng-Zhi,Chen, Zhen-Lin,Tarn, Ching,&Dong, Meng-Qiu.(2023).Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers.JOURNAL OF PROTEOME RESEARCH,22(8),2593-2607.
MLA	Cao, Yong,et al."Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers".JOURNAL OF PROTEOME RESEARCH 22.8(2023):2593-2607.