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PXD012109

PXD012109 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlepLink 2: A high-speed search engine with systematic evaluation for proteome-scale identification of cross-linked peptides
DescriptionCrosslinking 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:49:58.460.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterZhenlin Chen
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-12-19 02:09:38ID requested
12019-07-26 03:33:04announced
22019-07-26 03:47:18announcedUpdated publication reference for DOI(s): 10.1038/s41467-019-11337-z.
32019-08-12 07:33:03announcedUpdated publication reference for DOI(s): 10.1038/s41467-019-11337-z.
42023-11-14 08:49:59announced2023-11-14: Updated project metadata.
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: E.coli, QEHF
Contact List
Si-Min He
contact affiliationInstitute of Computing Technology, CAS
contact emailsmhe@ict.ac.cn
lab head
Zhenlin Chen
contact affiliationInstitute of Computing Technology, CAS
contact emailchenzhenlin@ict.ac.cn
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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