Optimization of Methods for the Quantitative Analysis of Global Cell Surface Proteome and Cell Surface Polarization

The cell surface proteome of polarized epithelial cells plays a central role in barrier function, signaling, and vectorial transport, yet the quantitative characterization of their surface proteins remains technically challenging. We developed an optimized chemoproteomic strategy specifically tailored to studying the surface proteins of polarized cells while keeping membrane integrity intact. By applying a disulfide-linked membrane-impermeable biotin reagent, labeling was restricted to extracellular regions of transmembrane proteins (TMPs) and secreted proteins, thereby minimizing contributions from intracellular contaminants. Following biotinylated peptide-level or protein-level enrichment and mass spectrometric analysis, we systematically compared data-dependent (DDA) and data-independent acquisition (DIA) approaches, showing that while DIA increases proteome coverage, DDA more reliably identifies biotinylated peptides in our studies. To ensure robustness, we established replicate-based normalization and contaminant-aware quality control metrics that minimize biases from proteins in cell culture medium and damaged cells. The application of the workflow to Madin-Darby canine kidney (MDCK) II epithelial monolayers enabled the large-scale quantification of apical versus basolateral domains, yielding over 2100 proteins, with 235 showing significant polarized distribution, in agreement with known biology. This method offers high specificity for the extracellular labeling and quantitative resolution of cell surface protein (CSP) polarization, providing a powerful platform for studying epithelial biology and identifying extracellular epitopes relevant to diagnostics and therapeutic targeting.