Quantitative Native Proteomics by Capillary Zone Electrophoresis-Mass Spectrometry

Accurately measuring complexoform dynamics (i.e., composition and/or abundance changes) in cells is vital for advancing fundamental and translational research. In this work, we present a pilot study establishing capillary zone electrophoresis (CZE)-mass spectrometry (MS)-based quantitative native proteomics to determine significant changes in complexoform abundance during the transition from logarithmic to stationary phase growth in <i>Escherichia coli</i>. The approach integrates (1) efficient and fast native CZE-MS to obtain the mass and signal intensity of complexoforms for label-free quantification, (2) in-source collision-induced dissociation, enabling informative fragmentation that reveals oligomeric states, and (3) denatured top-down proteomics for the identification of proteoforms, which form the complexoforms. We revealed differentially expressed complexoforms during the growth of <i>Escherichia coli</i>. For example, the glutamate decarboxylase beta hexamer (∼317 kDa) exhibits a significantly higher abundance at the stationary phase, which aligns with its biological function. This work represents the first quantitative native proteomics study using online native CZE-MS.