PXD067243

PXD067243 is an original dataset announced via ProteomeXchange.

Title	Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo
Description	Advancement in fluorescence imaging techniques enables the study of protein dynamics and localization with unprecedented spatiotemporal resolution. However, current imaging tools are unable to elucidate dynamic protein interactomes underlying imaging observations. In contrast, proteomics tools such as proximity labeling enable the analysis of protein interactomes at a single time point but lack information about protein dynamics. We herein developed Silicon-rhodamine-enabled Identification (SeeID) for near-infrared light controlled proximity labeling that could bridge the gap between imaging and proximity labeling. SeeID was benchmarked through characterization of various organelle-specific proteomes and the KRAS protein interactome. The fluorogenic nature of SiR allows for intracellular proximity labeling with high subcellular specificity. Leveraging SiR as both a fluorophore and a photocatalyst, we developed a protocol that allows the study of dynamic protein interactomes of Parkin during mitophagy. We discovered the association of the proteasome complex with Parkin at early time points, indicating the involvement of the ubiquitin-proteasome system for protein degradation in the early phase of mitophagy. In addition, by virtue of the deep tissue penetration of near-infrared light, we achieved spatiotemporally controlled proximity labeling in vivo across the mouse brain cortex with a labeling depth of ~2 mm using an off-the-shelf 660 nm LED light set-up.
HostingRepository	iProX
AnnounceDate	2025-08-11
AnnouncementXML	Submission_2025-09-11_20:11:25.467.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenjing Wang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-11 20:04:54	ID requested
1	2025-08-11 20:05:14	announced
⏵ 2	2025-09-11 20:11:26	announced	2025-09-12: Add info

Wang W, Guo H, Yan X, Pan X, Wang X, Rong Y, Bai Z, Zhang L, Wu Z, Zhao X, Huang W, Qin W, Chu L, Silicon-rhodamine-enabled identification for near-infrared light controlled proximity labeling in vitro and in vivo. Nat Commun, 16(1):8134(2025) [pubmed]

submitter keyword: proximity labeling, Silicon-rhodamine

Wei Qin
contact affiliation	Tsinghua University
contact email	weiqin@mail.tsinghua.edu.cn
lab head
Wenjing Wang
contact affiliation	Tsinghua University
contact email	wenjing930@126.com
dataset submitter

iProX dataset URI