MassIVE MSV000099787

Partial Public PXD070462

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

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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 vg 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. [doi:10.25345/C5CV4C51B] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Mass spectrometry, proteomics, MG132, ML-792, TPP ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Phil Lorenzi, MD Anderson Cancer Center, United States
Submitting User: yxiong3mda
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