PXD060403-1

PXD060403 is an original dataset announced via ProteomeXchange.

Title	Data-independent acquisition approach for comprehensive ubiquitinome profiling in targeted protein degradation
Description	Targeted protein degradation (TPD) has emerged as a highly promising therapeutic strategy for a wide range of diseases, including cancer and neurodegenerative disorders. The ubiquitin-proteasome system, which is responsible for protein degradation, plays a critical role in this process. Gaining comprehensive insights into the landscape of cellular ubiquitylation events is essential for the development of selective and efficient targeted protein degradation approaches. In recent years, data-independent acquisition (DIA) approach has gained significant popularity as a robust and unbiased approach for quantitative proteomics. By leveraging DIA, we have developed a cutting-edge workflow that utilizes diGly antibody-based enrichment followed by an optimized Orbitrap-based DIA method for the identification of ubiquitylated peptides. Through the implementation of our workflow, we have identified over 40,000 diGly precursors corresponding to more than 7,000 proteins in a single measurement from cells exposed to a proteasome inhibitor, highlighting an exceptional throughput. By applying our optimized workflow, we successfully identify ubiquitylation sites on substrate proteins in various TPD approaches, thereby helping establish mode of action for TPD. Our workflow therefore holds tremendous potential for rapidly establishing mode of action for various TPD modalities, such as for PROTACs and molecular glues.
HostingRepository	PRIDE
AnnounceDate	2026-06-09
AnnouncementXML	Submission_2026-06-09_07:30:32.094.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gajanan Sathe
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-31 10:20:29	ID requested
⏵ 1	2026-06-09 07:30:32	announced

Dataset with its publication pending

submitter keyword: ubiquitinome, PP2CA,dTAG

Dr Prof Gopal Sapkota
contact affiliation	MRC PPU University of Dundee
contact email	g.sapkota@dundee.ac.uk
lab head
Gajanan Sathe
contact affiliation	Centre for Targeted Protein Degradation (CeTPD) University of Dundee
contact email	gsathe001@dundee.ac.uk
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/2026/06/PXD060403

PRIDE project URI

• PRIDE
  1. PXD060403
     1. Label: PRIDE project
     2. Name: Data-independent acquisition approach for comprehensive ubiquitinome profiling in targeted protein degradation