PXD024253

PXD024253 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-18 22:00:09	ID requested
⏵ 1	2021-07-28 22:25:56	announced

Dataset with its publication pending

submitter keyword: Chemical crosslinking, XL-MS, Retention time, proteome-wide cross-link identification

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

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PRIDE project URI

• PRIDE
  1. PXD024253
     1. Label: PRIDE project
     2. Name: Retention time as an extra dimension for proteome-wide cross-link identification