PXD064185

PXD064185 is an original dataset announced via ProteomeXchange.

Title	Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts (solubility proteomics)
Description	Mass spectrometry (MS)-based proteomics has become indispensable for high-throughput quantitation of protein expression. However, protein function is regulated by a variety of factors beyond abundance alone. Here, we optimized narrow-window, data-independent ac-quisition (nDIA) MS with 3% DMSO as a supercharging co-solvent, boosting signal intensity by up to 56% and enabling identification of ~9,600 proteins from 1 µg of HeLa digest with a 15 min gradient. Using this methodology, we quantified solubility and abundance changes in 8,694 pro-teins across three cell lines following short-term treatment with the proteasome inhibitor MG132 and the SUMO-activating enzyme inhibitor ML-792. MG132 affected the solubility of 1,723 pro-teins and the abundance of 374, and ML-792 impacted 1,294 and 288, respectively. The drugs elicited distinct and sometimes opposing solubility shifts; For instance, MG132 insolubilized HSF1, ML-792 solubilized SP100 and insolubilized PLOR3G, and SMAD2 showed opposite responses to those two treatments. These results reveal widespread, drug-induced remodeling of the pro-tein solubility landscape and establish solubility profiling by nDIA-MS as a robust and broadly ap-plicable platform for uncovering protein state transitions and cellular responses to perturbation.
HostingRepository	PRIDE
AnnounceDate	2026-01-13
AnnouncementXML	Submission_2026-01-12_16:49:52.360.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yun Xiong
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-22 02:56:51	ID requested
⏵ 1	2026-01-12 16:49:52	announced

Dataset with its publication pending

submitter keyword: ML-792,Proteome, solubility shift, MG132

Philip L. Lorenzi
contact affiliation	The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA
contact email	yxiong3@mdanderson.org
lab head
Yun Xiong
contact affiliation	UT. MD. Anderson Cancer Center
contact email	yxiong3@mdanderson.org
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/2026/01/PXD064185

PRIDE project URI

• PRIDE
  1. PXD064185
     1. Label: PRIDE project
     2. Name: Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts (solubility proteomics)