Benchmarking of Quantitative Proteomics Workflows for Limited Proteolysis Mass Spectrometry.

ABSTRACT: Limited proteolysis coupled with mass spectrometry (LiP-MS) has emerged as a powerful technique for detecting protein structural changes and drug-protein interactions on a proteome-wide scale. However, there is no consensus on the best quantitative proteomics workflow for analyzing LiP-MS data. In this study, we comprehensively benchmarked two major quantification approaches-data-independent acquisition (DIA) and tandem mass tag (TMT) isobaric labeling-in combination with LiP-MS, using a drug-target deconvolution assay as a model system. Our results show that while TMT labeling enabled the quantification of more peptides and proteins with lower coefficients of variation, DIA-MS exhibited greater accuracy in identifying true drug targets and stronger dose-response correlation in peptides of

SUBMITTER: Koudelka T 

PROVIDER: S-EPMC12022698 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature