title: 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.
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.|University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Sheng-Bo
authors.initials: SB
authors.lastname: Fan
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.|University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Meng
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Lu
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.|University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.|University of the Chinese Academy of Sciences, Beijing, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Yang
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Chi
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.
authors.forename: Rui-Xiang
authors.initials: RX
authors.lastname: Sun
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Meng-Qiu
authors.initials: MQ
authors.lastname: Dong
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China.
authors.forename: Si-Min
authors.initials: SM
authors.lastname: He
mesh_terms: D003432:Cross-Linking Reagents / Q000737:chemistry*; D017408:Guidelines as Topic; D020407:Internet; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis*; D057386:Search Engine; D014584:User-Computer Interface
chemical_list: D003432:Cross-Linking Reagents; D010455:Peptides
keywords: cross-linking; mass spectrometry; pLink