Using pLink to Analyze Cross-Linked Peptides.

Using pLink to Analyze Cross-Linked Peptides. Curr Protoc Bioinformatics. 2015;49:8.21.1-8.21.19 Authors: Fan SB, Meng JM, Lu S, Zhang K, Yang H, Chi H, Sun RX, Dong MQ, He SM 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. © 2015 by John Wiley & Sons, Inc. PMID: 25754995 [PubMed - in process]
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research