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A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides by 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; Si-Min He is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides about?
## 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, ^15^N 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.
Who reads A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- 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; Si-Min He
- Publisher
- Springer Science and Business Media LLC
- Published
- 2019
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)