PXD024253 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Retention time as an extra dimension for proteome-wide cross-link identification |
Description | Chemical crosslinking methods have not been successfully applied to protein-protein interaction discovery mainly due to the computation complexity (O (n2)) issue. In a previous report, we proposed a decision tree searching strategy which can reduce complexity by orders of magnitude. In this study, we found that the mono-linked peptides carry out the information of the retention time of the cross-linked pairs, therefore the retention time of cross-linked peptide pairs can be predicted accurately. By utilizing the obtained retention time information, the false positive rate can be reduced by around 86% with a sensitivity loss of 12%. The method was successfully applied to the identification of inter cross-links obtained from E. coli cell lysate crosslinked by a newly synthesized enrichable crosslinker. |
HostingRepository | PRIDE |
AnnounceDate | 2021-07-29 |
AnnouncementXML | Submission_2021-07-28_22:25:55.923.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD024253 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Hongli Chen |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-02-18 22:00:09 | ID requested | |
⏵ 1 | 2021-07-28 22:25:56 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Chemical crosslinking, XL-MS, Retention time, proteome-wide cross-link identification |
Contact List
Hongli Chen |
contact affiliation | Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China |
contact email | chenhl@shanghaitech.edu.cn |
lab head | |
Hongli Chen |
contact affiliation | ShanghaiTech University |
contact email | chenhl@shanghaitech.edu.cn |
dataset submitter | |
Full Dataset Link List
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/2021/07/PXD024253 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD024253
- Label: PRIDE project
- Name: Retention time as an extra dimension for proteome-wide cross-link identification