PXD012109

PXD012109 is an original dataset announced via ProteomeXchange.

Title	pLink 2: A high-speed search engine with systematic evaluation for proteome-scale identification of cross-linked peptides
Description	Crosslinking mass spectrometry (CXMS) is a powerful technique to study protein structures and interactions. However, software tools for CXMS data analysis suffer from poor speed and credibility, especially at a proteome scale. Here, we introduce pLink 2, a search engine with higher speed and credibility for proteome-scale identification of crosslinked peptides. With a novel two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, four new analysis methods, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, were designed to evaluate the credibility of ten state-of-the-art search engines, this systematic evaluation showed that pLink 2 achieved the highest precision and sensitivity. Finally, four whole-cell lysate datasets, previously analysed by pLink 1 in months, were reanalysed by pLink 2 only in days, with up to 27.4% more crosslinks identified. The new search engine pLink 2 and the new evaluation methods are well positioned to become new benchmarks in the CXMS research field.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:58.460.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhenlin Chen
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-19 02:09:38	ID requested
1	2019-07-26 03:33:04	announced
2	2019-07-26 03:47:18	announced	Updated publication reference for DOI(s): 10.1038/s41467-019-11337-z.
3	2019-08-12 07:33:03	announced	Updated publication reference for DOI(s): 10.1038/s41467-019-11337-z.
⏵ 4	2023-11-14 08:49:59	announced	2023-11-14: Updated project metadata.

Chen ZL, Meng JM, Cao Y, Yin JL, Fang RQ, Fan SB, Liu C, Zeng WF, Ding YH, Tan D, Wu L, Zhou WJ, Chi H, Sun RX, Dong MQ, He SM, A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat Commun, 10(1):3404(2019) [pubmed]

curator keyword: Technical

submitter keyword: E.coli, QEHF

Si-Min He
contact affiliation	Institute of Computing Technology, CAS
contact email	smhe@ict.ac.cn
lab head
Zhenlin Chen
contact affiliation	Institute of Computing Technology, CAS
contact email	chenzhenlin@ict.ac.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/07/PXD012109

PRIDE project URI

• PRIDE
  1. PXD012109
     1. Label: PRIDE project
     2. Name: pLink 2: A high-speed search engine with systematic evaluation for proteome-scale identification of cross-linked peptides