PXD012109 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD012109
- Label: PRIDE project
- Name: pLink 2: A high-speed search engine with systematic evaluation for proteome-scale identification of cross-linked peptides