PXD056778

PXD056778 is an original dataset announced via ProteomeXchange.

Title	Energy transfer photoproximity labelling in live cells using an organic cofactor
Description	Photocatalytic proximity labelling has recently emerged as a powerful tool to resolve a wide variety of biomolecular and cellular interactions. While the use of high-resolution probe species, such as diazirines, enables cell-surface protein labelling with nanometre precision by generating highly reactive intermediates, intracellular applications are limited either by the intrinsic toxicity of frequently employed photocatalysts or lower resolution when long-lived reactive intermediates are used. In this work, we describe the discovery and application of an organic flavin cofactor derivative, deazaflavin, capable of diazirine activation to form carbenes through triplet energy transfer and offers unparalleled biocompatibility. We demonstrate deazaflavin-diazirine energy transfer labelling (DarT-labelling) not only allows for targeted extracellular scenarios using antibody conjugates but, most importantly, for intracellular interactome mapping of cell-penetrating peptides (CPPs). We successfully mapped the localisation of two popular polyarginine CPPs and identified potential key membrane interactors. Furthermore, we showed the applicability of DarT-labelling over extended time by mapping the intracellular trafficking of a stable cyclic derivative to reveal its eventual exocytosis from the cell. We envision DarT-labelling has the unmet potential to enable detailed profiling of intracellular dynamics across diverse biological systems with unprecedented spatiotemporal control.
HostingRepository	PRIDE
AnnounceDate	2025-12-08
AnnouncementXML	Submission_2025-12-07_18:28:07.267.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Max Ruwolt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-14 03:33:22	ID requested
⏵ 1	2025-12-07 18:28:08	announced

Crocker LB, Arafiles JVV, M, ü, chler JM, Ruwolt M, Kemnitz-Hassanin K, Ro, ß, mann K, Stieger CE, Liu F, Archipowa N, Kutta RJ, Hackenberger CPR, Energy-transfer photoproximity labelling in live cells using an organic cofactor. Nat Chem, 17(12):1928-1940(2025) [pubmed]

10.1038/s41557-025-01931-8;

submitter keyword: photoproximity, diazirine, LFQ, DarT

Christian Hackenberger
contact affiliation	Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
contact email	Hackenbe@fmp-berlin.de
lab head
Max Ruwolt
contact affiliation	Leibniz-Forschungsinstitut for Molecular Pharmacology
contact email	ruwolt@fmp-berlin.de
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/2025/12/PXD056778

PRIDE project URI

• PRIDE
  1. PXD056778
     1. Label: PRIDE project
     2. Name: Energy transfer photoproximity labelling in live cells using an organic cofactor