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A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides
Open accessAbstract
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.
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Metadata
- Authors
- Chen, Z.-L., Meng, J.-M., Cao, Y., Yin, J.-L., Fang, R.-Q., Fan, S.-B., Liu, C., Zeng, W.-F., Ding, Y.-H., Tan, D., Wu, L., Zhou, W.-J., Chi, H., Sun, R.-X., Dong, M.-Q., & He, S.-M.
- Venue
- Nature Communications
- Published
- 2019-07-30
- Volume
- 10
- Issue
- 1
- Pages
- 3404-3404
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2966215858
- Cited by
- 552
- References
- 6
- FWCI
- 20.18
- Type
- journal article
- Language
- en
- Open access
- gold
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