Improved drug target deconvolution with PISA-DIA using an extended, overlapping temperature gradient

Emery-Corbin, SJ; Yousef, JM; Adhikari, S; Sumardy, F; Nhu, D; van Delft, MF; Lessene, G; Dziekan, J; Webb, AI; Dagley, LF

Author(s): Emery-Corbin, SJ; Yousef, JM; Adhikari, S; Sumardy, F; Nhu, D; van Delft, MF; Lessene, G; Dziekan, J; Webb, AI; Dagley, LF;
Details: Publication Year 2024-05-20,Volume 24,Issue #16,Page e2300644
Journal Title: Proteomics
Abstract: Thermal proteome profiling (TPP) is a powerful tool for drug target deconvolution. Recently, data-independent acquisition mass spectrometry (DIA-MS) approaches have demonstrated significant improvements to depth and missingness in proteome data, but traditional TPP (a.k.a. CEllular Thermal Shift Assay "CETSA") workflows typically employ multiplexing reagents reliant on data-dependent acquisition (DDA). Herein, we introduce a new experimental design for the Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA). We highlight the proteome coverage and sensitivity achieved by using multiple overlapping thermal gradients alongside DIA-MS, which maximizes efficiencies in PISA sample concatenation and safeguards against missing protein targets that exist at high melting temperatures. We demonstrate our extended PISA-DIA design has superior proteome coverage as compared to using tandem-mass tags (TMT) necessitating DDA-MS analysis. Importantly, we demonstrate our PISA-DIA approach has the quantitative and statistical rigor using A-1331852, a specific inhibitor of BCL-xL. Due to the high melt temperature of this protein target, we utilized our extended multiple gradient PISA-DIA workflow to identify BCL-xL. We assert our novel overlapping gradient PISA-DIA-MS approach is ideal for unbiased drug target deconvolution, spanning a large temperature range whilst minimizing target dropout between gradients, increasing the likelihood of resolving the protein targets of novel compounds.
Publisher: Wiley
Keywords: Proteome Integral Solubility Alteration; data independent acquisition (DIA); mass spectrometry; protein stability; proteomics; target engagement; thermal proteome profiling
Research Division(s): Blood Cells And Blood Cancer; Chemical Biology; Infectious Diseases And Immune Defence; Advanced Technology And Biology
PubMed ID: 38766901
Publisher's Version: https://doi.org/10.1002/pmic.202300644
Open Access at Publisher's Site: https://doi.org/10.1002/pmic.202300644
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2024-06-24 11:25:19

Last Modified: 2024-08-23 03:09:52