PXD047979 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Super-resolution proximity labeling method with enhanced direct identification of biotinylation sites |
Description | Promiscuous labeling enzymes, such as APEX2 or TurboID, are commonly used in in situ biotinylation studies of subcellular proteomes or protein-protein interactions. Although the conventional approach of enriching biotinylated proteins is widely implemented, in-depth identification of specific biotinylation sites remains challenging, and current approaches are technically demanding with low yields. A novel method to systematically identify specific biotinylation sites for LC-MS analysis followed by proximity labeling showed excellent performance compared with that of related approaches in terms of identification depth with high enrichment power. The systematic identification of biotinylation sites enabled a simpler and more efficient experimental design to identify subcellular localized proteins within membranous organelles. Applying this method to the processing body (PB), a non-membranous organelle, successfully allowed unbiased identification of PB core proteins, including novel candidates. We anticipate that our newly developed method will replace the conventional method for identifying biotinylated proteins labeled by promiscuous labeling enzymes. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:41:01.406.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Sanghee Shin |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | biotinylated residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-12-19 21:07:58 | ID requested | |
1 | 2024-05-22 02:09:30 | announced | |
⏵ 2 | 2024-10-22 06:41:07 | announced | 2024-10-22: Updated project metadata. |
Publication List
Shin S, Lee SY, Kang MG, Jang DG, Kim J, Rhee HW, Kim JS, Super-resolution proximity labeling with enhanced direct identification of biotinylation sites. Commun Biol, 7(1):554(2024) [pubmed] |
10.1038/s42003-024-06112-w; |
Keyword List
submitter keyword: biotinylation site, APEX2, TurboID, LC-MS, membrane protein topology, BioID,Proximity labeling |
Contact List
Jong-Seo Kim |
contact affiliation | School of Biological Sciences, Seoul National University, Seoul 08826, Korea |
contact email | jongseokim@snu.ac.kr |
lab head | |
Sanghee Shin |
contact affiliation | Seoul National University |
contact email | sunnyshin54@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD047979
- Label: PRIDE project
- Name: Super-resolution proximity labeling method with enhanced direct identification of biotinylation sites