Using pLink to Analyze Cross-Linked Peptides

Current Protocols in Bioinformatics
Sheng-Bo FanSi-Min He

Abstract

pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink.

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Mar 16, 2017·Molecular & Cellular Proteomics : MCP·Lili CaiFuchu He
Aug 2, 2017·Expert Review of Proteomics·Evelyne MaesStefan Clerens
Feb 13, 2019·Current Protocols in Protein Science·Hsin-Yao Tang, David W Speicher
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Jan 17, 2021·Molecular & Cellular Proteomics : MCP·Andreas LindenHenning Urlaub
Jul 7, 2020·Journal of Molecular Biology·Jin Joo KangNicole J Francis

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