Enhancing Top-Down Characterization of Membrane Proteoforms with C8-Functional Amine-Bridged Hybrid Monoliths

Comprehensive characterization of membrane proteins at the level of proteoforms in complex biological samples by top-down mass spectrometry (MS) is of vital importance in revealing their precise functions. However, severe peak broadening in the separation of hydrophobic membrane proteins, caused by resistance to mass transfer and strong adsorption on separation materials, leads to MS spectra overlap and signal suppression, which makes against the in-depth research on membrane proteoforms. Herein, C8-functional amine-bridged hybrid monoliths with an interconnected macroporous structure were developed by the in situ one-step sol-gel reaction of triethoxy(octyl)silane and bis[3-(trimethoxysilyl)propyl]amine in capillaries. Due to the unique macroporous structure and bridged secondary amino groups in the framework, the monolith possessed reduced resistance to mass transfer, low nonspecific adsorption, and electrostatic repulsion to membrane proteins. These features tremendously alleviated peak broadening in the separation of membrane proteins, thus outperforming traditional reversed-phase columns in top-down characterization of membrane proteoforms. With this monolith, a total of 3100 membrane proteoforms were identified in the mouse hippocampus, representing the largest membrane proteoform database obtained by top-down analysis so far. The identified membrane proteoforms revealed abundant information, including combinatorial post-translational modifications (PTMs), truncation, and transmembrane domains. Furthermore, the proteoform information was integrated into the interaction network of membrane protein complexes involved in oxidative phosphorylation processing, opening up new opportunities to uncover more detailed molecular basis and interaction in the biological processes.