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Chen, Zhen-Lin; Meng, Jia-Ming; Cao, Yong; Yin, Ji-Li; Fang, Run-Qian; Fan, Sheng-Bo; Liu, Chao; Zeng, Wen-Feng; Ding, Yue-He; Tan, Dan; Wu, Long; Zhou, Wen-Jing; Chi, Hao; Sun, Rui-Xiang; Dong, Meng-Qiu; He, Si-Min
Nature communications, 07/2019, Letnik: 10, Številka: 1Journal Article
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, 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.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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in: SICRIS
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