Using pLink to Analyze Cross‐Linked Peptides

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.

Discovering cellular protein‐protein interactions: Technological strategies and opportunities

“…The standard identification algorithms of MS are not useful in most cases, although the constantly increasing resolution of MS instruments, the use of cleavable cross‐linkers, and the integration of affinity purification can reduce a part of the problem. Ample alternative data analysis tools exist, but all of them are specialized in only a small variety of data types …”

“…Ample alternative data analysis tools exist, but all of them are specialized in only a small variety of data types. 158,191,[194][195][196][197][198][199][200][201][202][203][204][205]…”

Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics

“…The most popular and commonly used software for MS and MS/MS data analysis of cross-linked products are General Protein/Mass Analysis for Windows (GPMAW) [60], xComb [17], Popitam [61], X!Link [62,63], xQuest [8,31], XLink-Identifier [40], pLink [16,31,64], and more recently, StavroX [65] and MeroX [56]. Unique properties and applications of these software tools are described in Table 1.…”

Chemical Cross-linking Mass Spectrometry for Profiling Protein Structures and Protein-Protein Interactions

“…Many MS and MS/MS search algorithms have been developed for different types of cross-linkers and their applications. xComb [13], MassMatrix [14], StarvroX [15], XLinkidentifier [16], and pLink [17,18] are commonly used for non-cleavable homobifunctional or heterobifunctional cross-linkers. By importing cross-linker information and protein FASTA database, xComb creates a linearized and concatenated cross-linked peptide database that can be used as a common search engine.…”