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bioRxiv · 10.1101/2021.12.31.474672

SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale

Zhang, W.·Gong, P.·Shan, Y.·Zhao, L.·Hu, H.·Wei, Q.·Liang, Z.·Liu, C.·Zhang, L.·Zhang, Y.
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Abstract

We developed SpotLink software for identifying site non-specific cross-links at the proteome scale. Contributed by the dual pointer dynamic pruning (DPDP) algorithm and the quality control of cross-linking sites, SpotLink identified more than 3000 cross-links from human proteome database with rich site information in a few days. We demonstrated that SpotLink outperformed other approaches in terms of sensitivity and precision on a simulated dataset and a protein complexes dataset with known structures. Additionally, we discovered some valuable protein-protein interaction (PPI) information contained in the protein complexes dataset and HeLa dataset, indicating the unique identification advantages of site non-specific cross-linking. The excellent performance of SpotLink will increase the usage of site non-specific cross-linking in the near future. SpotLink is publicly available on GitHub [https://github.com/DICP1810/SpotLink].

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Zhang, W., Gong, P., Shan, Y., Zhao, L., Hu, H., Wei, Q., Liang, Z., Liu, C., Zhang, L., Zhang, Y.. 2022-01-02. SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale. https://doi.org/10.1101/2021.12.31.474672

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