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

Zhen-Lin Chen, Jia-Ming Meng, Yong Cao, Ji-Li Yin, Run-Qian Fang, Sheng-Bo Fan, Chao Liu, Wen-Feng Zeng, Yue-He Ding, Dan Tan, Long Wu, Wen-Jing Zhou, Hao Chi, Rui-Xiang Sun, Meng-Qiu Dong () and Si-Min He ()
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Zhen-Lin Chen: Institute of Computing Technology, CAS
Jia-Ming Meng: Institute of Computing Technology, CAS
Yong Cao: National Institute of Biological Sciences
Ji-Li Yin: Institute of Computing Technology, CAS
Run-Qian Fang: Institute of Computing Technology, CAS
Sheng-Bo Fan: Institute of Computing Technology, CAS
Chao Liu: Institute of Computing Technology, CAS
Wen-Feng Zeng: Institute of Computing Technology, CAS
Yue-He Ding: National Institute of Biological Sciences
Dan Tan: National Institute of Biological Sciences
Long Wu: Institute of Computing Technology, CAS
Wen-Jing Zhou: Institute of Computing Technology, CAS
Hao Chi: Institute of Computing Technology, CAS
Rui-Xiang Sun: National Institute of Biological Sciences
Meng-Qiu Dong: National Institute of Biological Sciences
Si-Min He: Institute of Computing Technology, CAS

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract 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 ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15N 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, re-analysis 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.

Date: 2019
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DOI: 10.1038/s41467-019-11337-z

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