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Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts (co-solvent)

ABSTRACT: Mass spectrometry (MS)-based proteomics has become indispensable for high-throughput quantitation of protein expression. However, protein function is regulated by a vari-ety of factors beyond abundance alone. Here, we optimized narrow-window, data-independent acquisition (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 proteins across three cell lines following short-term treatment with the proteasome in-hibitor MG132 and the SUMO-activating enzyme inhibitor ML-792. MG132 affected the solubil-ity of 1,723 proteins and the abundance of 374, and ML-792 impacted 1,294 and 288, respec-tively. 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 wide-spread, drug-induced remodeling of the protein solubility landscape and establish solubility profiling by nDIA-MS as a robust and broadly applicable platform for uncovering protein state transitions and cellular responses to perturbation.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yun Xiong

LAB HEAD: Philip L. Lorenzi

PROVIDER: PXD064180 | Pride | 2026-01-11

REPOSITORIES: Pride

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			Action	DRS
	091624_OptmzDIA_15m_0p001mNBA_Hela200ng_1.raw	Raw
	091624_OptmzDIA_15m_0p001mNBA_Hela200ng_2.raw	Raw
	091624_OptmzDIA_15m_0p001mNBA_Hela200ng_3.raw	Raw
	091624_OptmzDIA_15m_0p01mNBA_Hela200ng_1.raw	Raw
	091624_OptmzDIA_15m_0p01mNBA_Hela200ng_2.raw	Raw

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Supercharging-Enhanced nDIA-MS Enables Global Profiling of Drug-Induced Proteome Solubility Shifts (solubility proteomics)

Project 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.

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