Comparative Analysis of Chemical Cross-Linking Mass Spectrometry Data Indicates That Protein STY Residues Rarely React with N-Hydroxysuccinimide Ester Cross-Linkers
文献类型：期刊论文
| 作者 | Cao, Yong2; Liu, Xin-Tong2; Mao, Peng-Zhi3,4; Chen, Zhen-Lin3,4; Tarn, Ching3,4; Dong, Meng-Qiu1,2 |
| 刊名 | JOURNAL OF PROTEOME RESEARCH
 |
| 出版日期 | 2023-07-26 |
| 卷号 | 22期号:8页码:2593-2607 |
| ISSN号 | 1535-3893 |
| 关键词 | CXMS XL-MS NHS ester cross-linker pLink xiSearch MeroX |
| DOI | 10.1021/acs.jproteome.3c00037 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| 出版者 | AMER CHEMICAL SOC |
| WOS记录号 | WOS:001036853500001 |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/21297]  |
| 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.Tsinghua Univ, Tsinghua Inst Multidisciplinary Biomed Res, Beijing 102206, Afghanistan 2.Natl Inst Biol Sci, Beijing 102206, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc Chinese Acad Sci, Beijing 100190, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 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. |
入库方式： OAI收割
来源：计算技术研究所
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