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 Escherichia coli. 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 Escherichia coli. 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.