Labeling Carboxyl Groups of Surface-Exposed Proteins Provides an Orthogonal Approach for Cell Surface Isolation

Quantitative profiling
of cell surface proteins is critically important
for the understanding of cell-cell communication, signaling, tissue
development, and homeostasis. Traditional proteomics methods are challenging
for cell surface proteins due to their hydrophobic nature and low
abundance, necessitating alternative methods to efficiently identify
and quantify this protein group. Here we established carboxyl-reactive
biotinylation for selective and efficient biotinylation and isolation
of surface-exposed proteins of living cells. We assessed the efficiency
of carboxyl-reactive biotinylation for plasma membrane proteins by
comparing it with a well-established protocol, amine-reactive biotinylation,
using SILAC (stable isotope labeling in cell culture). Our results
show that carboxyl-reactive biotinylation of cell surface proteins
is both more selective and more efficient than amine-reactive biotinylation.
We conclude that it is a useful approach, which is partially orthogonal
to amine-reactive biotinylation, allowing us to cast a wider net for
a comprehensive profiling of cell surface proteins.