PXD037678

PXD037678 is an original dataset announced via ProteomeXchange.

Title	Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome
Description	Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in Hela cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:02:32.986.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zheng Fu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-24 02:00:08	ID requested
1	2023-07-20 10:39:20	announced
⏵ 2	2023-11-14 09:02:35	announced	2023-11-14: Updated project metadata.

Zheng F, Yu C, Zhou X, Zou P, Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome. Nat Commun, 14(1):2978(2023) [pubmed]

submitter keyword: miniSOG SOPP3 proximity labeling photosensitive protein singlet oxygen

Peng Zou
contact affiliation	College of chemistry and molecular engineering, Peking University.
contact email	zoupeng@pku.edu.cn
lab head
Zheng Fu
contact affiliation	Peking University
contact email	amadeuszheng@pku.edu.cn
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/2023/07/PXD037678

PRIDE project URI

• PRIDE
  1. PXD037678
     1. Label: PRIDE project
     2. Name: Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome