A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

doi:10.1038/s41467-019-11337-z

	A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides
	Chen, Zhen-Lin 1,2; Meng, Jia-Ming 1,2; Cao, Yong 3; Yin, Ji-Li 1,2; Fang, Run-Qian 1,2; Fan, Sheng-Bo 1,2; Liu, Chao 1,2; Zeng, Wen-Feng 1,2; Ding, Yue-He 3; Tan, Dan 3; Wu, Long 1,2; Zhou, Wen-Jing 1,2; Chi, Hao 1,2; Sun, Rui-Xiang 3; Dong, Meng-Qiu 3; He, Si-Min 1,2
	2019-07-30
发表期刊	NATURE COMMUNICATIONS
ISSN	2041-1723
卷号	10 页码:12
摘要	We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is similar to 40 times faster than pLink 1 and 3 similar to 10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, N-15 metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, reanalysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
DOI	10.1038/s41467-019-11337-z
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[21475141] ; National Natural Science Foundation of China[31700727] ; National Natural Science Foundation of China[31470805] ; National Key Research and Development Program of China[2016YFA0501300] ; CAS Interdisciplinary Innovation Team[Y604061000]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000477860700010
出版者	NATURE PUBLISHING GROUP
引用统计	被引频次：342[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4543
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Dong, Meng-Qiu; 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,Meng, Jia-Ming,Cao, Yong,et al. A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides[J]. NATURE COMMUNICATIONS,2019,10:12.
APA	Chen, Zhen-Lin.,Meng, Jia-Ming.,Cao, Yong.,Yin, Ji-Li.,Fang, Run-Qian.,...&He, Si-Min.(2019).A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides.NATURE COMMUNICATIONS,10,12.
MLA	Chen, Zhen-Lin,et al."A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides".NATURE COMMUNICATIONS 10(2019):12.