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PXD024253

PXD024253 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRetention time as an extra dimension for proteome-wide cross-link identification
DescriptionChemical 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.
HostingRepositoryPRIDE
AnnounceDate2021-07-29
AnnouncementXMLSubmission_2021-07-28_22:25:55.923.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD024253
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterHongli Chen
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationListiodoacetamide derivatized residue
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-02-18 22:00:09ID requested
12021-07-28 22:25:56announced
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 affiliationShanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
contact emailchenhl@shanghaitech.edu.cn
lab head
Hongli Chen
contact affiliationShanghaiTech University
contact emailchenhl@shanghaitech.edu.cn
dataset submitter
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Dataset FTP location
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