PXD047979

PXD047979 is an original dataset announced via ProteomeXchange.

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

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.

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;

submitter keyword: biotinylation site, APEX2, TurboID, LC-MS, membrane protein topology, BioID,Proximity labeling

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

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/2024/05/PXD047979

PRIDE project URI

• PRIDE
  1. PXD047979
     1. Label: PRIDE project
     2. Name: Super-resolution proximity labeling method with enhanced direct identification of biotinylation sites