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

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 s...

Full description

Saved in:
Bibliographic Details
Published inbioRxiv
Main Authors Zhang, Weijie, Gong, Pengyun, Shan, Yichu, Zhao, Lili, Hu, Honeke, Wei, Qiushi, Liang, Zhen, Liu, Chao, Zhang, Lihua, Zhang, Yukui
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 02.01.2022
Subjects
Datasets
Protein interaction
Proteins
Proteomes
Quality control
Online AccessGet full text

Cover

More Information
Summary: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]. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://github.com/DICP1810/SpotLink
DOI:10.1101/2021.12.31.474672