PXD076830-1

PXD076830 is an original dataset announced via ProteomeXchange.

Title	Deazaflavin-Diazirine Energy-Transfer (DarT) Photoproximity Labelling of the HER2 Interactome Using Antibody Conjugates
Description	Elucidating protein-protein interactions plays a crucial part in understanding disease mecha-nisms and advancing pharmacological research. Photocatalytic proximity labelling using anti-body–catalyst conjugates enables the highly target-specific analysis of protein-protein inter-actions on the cell surface without altering the native cellular state through genetic manipu-lation. Here, we describe an extension of the deazaflavin–diazirine energy-transfer (DarT) labelling platform through the development and evaluation of trastuzumab–deazaflavin (Tra–dFl) conjugates for mapping the extracellular microenvironment of human epidermal growth factor receptor 2 (HER2). Four Tra–dFl conjugates were synthesised via azide–DBCO click chemistry, varying in PEG linker size and catalyst loading: Tra–PEG0–dFl, Tra–PEG6–dFl, Tra–PEG12–dFl, and Tra-bis-dFl exhibiting a branched linker for dual attachment. Imaging and proteomic pulldown experiments revealed that linker size influences biotinylation effi-ciency and proteomic enrichment, resulting in Tra–PEG12–dFl to emerge as the most effec-tive construct, enabling enrichment of cancer-associated cell surface proteins in HER2-positive SK-BR-3 cells. Evaluation of catalyst valency using a branched linker resulted in fewer enriched proteins, suggesting that linker architecture is more critical for conjugate perfor-mance than increased catalyst loading. Together, these findings provide guidelines for anti-body-based deazaflavin conjugates and expand the applicability of DarT labelling for target-directed surfaceome mapping.
HostingRepository	PRIDE
AnnounceDate	2026-08-04
AnnouncementXML	Submission_2026-08-04_03:05:23.415.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	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-09 18:09:04	ID requested
⏵ 1	2026-08-04 03:05:23	announced

Dataset with its publication pending

submitter keyword: None

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	Protein Biochemistry Institute for Chemistry and Biochemistry Freie Universität Berlin
contact email	ruwolt.max@fu-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/2026/08/PXD076830

PRIDE project URI

• PRIDE
  1. PXD076830
     1. Label: PRIDE project
     2. Name: Deazaflavin-Diazirine Energy-Transfer (DarT) Photoproximity Labelling of the HER2 Interactome Using Antibody Conjugates