SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale Article Swipe
Weijie Zhang
,
Pengyun Gong
,
Yichu Shan
,
Lili Zhao
,
Hongke Hu
,
Qiushi Wei
,
Zhen Liang
,
Chao Liu
,
Lihua Zhang
,
Yukui Zhang
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2021.12.31.474672
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2021.12.31.474672
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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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2021.12.31.474672
- https://www.biorxiv.org/content/biorxiv/early/2022/01/02/2021.12.31.474672.full.pdf
- OA Status
- green
- Cited By
- 2
- References
- 26
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4205688538
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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- DOI
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- Title
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SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scaleWork title
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-01-02Full publication date if available
- Authors
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Weijie Zhang, Pengyun Gong, Yichu Shan, Lili Zhao, Hongke Hu, Qiushi Wei, Zhen Liang, Chao Liu, Lihua Zhang, Yukui ZhangList of authors in order
- Landing page
-
https://doi.org/10.1101/2021.12.31.474672Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2022/01/02/2021.12.31.474672.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2022/01/02/2021.12.31.474672.full.pdfDirect OA link when available
- Concepts
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Proteome, Computer science, Identification (biology), Software, Computational biology, Data mining, Bioinformatics, Biology, Programming language, BotanyTop concepts (fields/topics) attached by OpenAlex
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2Total citation count in OpenAlex
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2024: 1, 2023: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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