Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts

Authors

Yun Xiong
Huimin Zhang
Lin Tan
Bo Wei
John N Weinstein
Philip L Lorenzi

Language

English

Publication Date

1-30-2026

Journal

Nature Communications

DOI

10.1038/s41467-026-69025-8

PMID

41617713

PMCID

PMC12979856

PubMedCentral® Posted Date

1-30-2026

PubMedCentral® Full Text Version

Author MSS

Abstract

Mass spectrometry (MS) is indispensable for high-throughput quantitation of protein expression. But protein function is regulated by factors beyond abundance alone. Here, we evaluate two supercharging reagents, dimethyl sulfoxide (DMSO) and m-nitrobenzyl alcohol (mNBA), in narrow-window data-independent acquisition (nDIA)-MS. DMSO markedly enhances MS signal and protein identification, whereas mNBA primarily increases peptide identifications. Optimizating nDIA-MS with 3% DMSO boosts signal intensity by up to 56%, enabling identification of ~9,600 proteins from 1 µg HeLa digest in 15 min. Using this methodology, we quantify solubility and abundance changes in 8,694 proteins across three cell lines following short-term treatment with the proteasome inhibitor MG132 and the SUMO-activating enzyme inhibitor ML-792. MG132 affects the solubility of 1,723 proteins and the abundance of 374, and ML-792 affects 1,294 and 288, respectively. The drugs elicit distinct and sometimes opposing solubility shifts; for instance, MG132 insolubilizes HSF1, ML-792 solubilizes SP100 and insolubilizes PLOR3G, and SMAD2 shows opposite responses to those two treatments. These results reveal widespread, drug-induced remodeling of the protein solubility landscape and establish solubility profiling by nDIA-MS as a broadly applicable platform for uncovering protein state transitions and cellular responses to perturbation.

Keywords

Humans, Proteome, Solubility, Leupeptins, Dimethyl Sulfoxide, HeLa Cells, Proteomics, Mass Spectrometry, Proteasome Inhibitors, Proteomics, Proteomics, Mass spectrometry

Published Open-Access

yes

Recommended Citation

Xiong, Yun; Zhang, Huimin; Tan, Lin; et al., "Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts" (2026). Faculty, Staff and Student Publications. 6775.
https://digitalcommons.library.tmc.edu/uthgsbs_docs/6775