PXD069438

PXD069438 is an original dataset announced via ProteomeXchange.

Title	Systematic Proteome-Wide Target Interrogation of PROTAC activity by High-Throughput DIA-MS on the Orbitrap Astral Platform
Description	An efficient degradation-based proteomics workflow was established using data-independent acquisition-mass spectrometry (DIA-MS) and the Orbitrap Astral platform to investigate the mode of actions (MOA) and on target specificity of bromodomain and extra-terminal (BET) protein-targeting PROTACs, MZ1 and dBET6. Human cancerous and noncancerous cell lines (HeLa, MDA-MB-231 and HEK293) were treated with 1 µM of the PROTACs and their respective negative control controls (cis-MZ1 and dBET6Me) for 1 h and 24 h. Following treatment, cell pellets were harvested, proteins were processed and analysed in a 96-well plate format to identify proteins dysregulated at each timepoint. This approach successfully identified the three BET family members, bromodomain containing proteins 2/3/4 (BRD2, BRD3, BRD4) as the primary targets of MZ1 and dBET6 from the total proteomes of 9,641, 8,157 and 8,988 quantified proteins in HEK293, HeLa and MDA-MB-231 cells, respectively, after short (1 h) treatment. Extended treatment (24 h) with MZ1 and dBET6 further revealed 51, 57 and 115 secondary proteins significantly perturbed (|log2 fold change (log2FC)| ≥ 1 and adjusted p (adj.p) ≤ 0.05) in HEK293, HeLa and MDA-MB-231 cells, respectively. Overall, this work demonstrates the feasibility of the developed approach for identifying direct PROTAC targets following short incubations, as well as elucidating downstream proteomic alterations upon prolonged treatment, surpassing the resolution achievable by traditional immunoblotting techniques.
HostingRepository	PRIDE
AnnounceDate	2026-03-07
AnnouncementXML	Submission_2026-03-07_03:07:35.858.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ghizal Siddiqui
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-14 04:49:23	ID requested
⏵ 1	2026-03-07 03:07:36	announced

Dataset with its publication pending

submitter keyword: proteomics, DIA-MS,Bromodomain containing proteins, Orbitrap Astral, proteolysis targeting chimeras

Manuela Jorg
contact affiliation	Medicinal Chemistry, Monash Institute of Pharmaceutica Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
contact email	Manuela.Jorg@monash.edu
lab head
Ghizal Siddiqui
contact affiliation	Monash University
contact email	ghizal.siddiqui@monash.edu
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/2026/03/PXD069438

PRIDE project URI

• PRIDE
  1. PXD069438
     1. Label: PRIDE project
     2. Name: Systematic Proteome-Wide Target Interrogation of PROTAC activity by High-Throughput DIA-MS on the Orbitrap Astral Platform