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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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Semi-supervised learning for peptide identification from shotgun proteomics datasets
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424
Structure of activated transcription complex Pol II–DSIF–PAF–SPT6
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JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy
Wang, X., Li, Y., Wu, Z., Wang, H., Tan, H., & Peng, J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.039586 · Cited by 194
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pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification
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Self-citationStructure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation
Vos, S. M., Farnung, L., Linden, A., Urlaub, H., & Cramer, P. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0437-1 · Cited by 160
Papier, K., Atkins, J. R., Tong, T. Y. N., Gaitskell, K., Desai, T., Ogamba, C. F., Parsaeian, M., Reeves, G. K., Mills, I. G., Key, T. J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48017-6 · Cited by 97
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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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- 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. (2019). A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nature Communications. https://doi.org/10.1038/s41467-019-11337-z
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