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

文献类型：期刊论文

作者Chen, Zhen-Lin1,2; Meng, Jia-Ming1,2; Cao, Yong3; Yin, Ji-Li1,2; Fang, Run-Qian1,2; Fan, Sheng-Bo1,2; Liu, Chao1,2; Zeng, Wen-Feng1,2; Ding, Yue-He3; Tan, Dan3
刊名NATURE COMMUNICATIONS
出版日期2019-07-30
卷号10页码:12
ISSN号2041-1723
DOI10.1038/s41467-019-11337-z
英文摘要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.
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
语种英语
WOS记录号WOS:000477860700010
出版者NATURE PUBLISHING GROUP
源URL[http://119.78.100.204/handle/2XEOYT63/4542]  
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.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
2.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, 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.

入库方式： OAI收割

来源：计算技术研究所

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