Improved T cell surfaceomics by depleting intracellularly labelled dead cells

Although the plasma membrane (PM) is among the most biologically important and therapeutically targeted cellular compartments, it is among the most challenging to faithfully capture using proteomic approaches. The quality of quantitative surfaceomics data depends heavily on the effectiveness of the cell surface enrichment used during sample preparation. Enrichment improves sensitivity for low abundance PM proteins and ensures that the changes detected reflect PM expression changes rather than whole cell changes. Cell surface biotinylation with PM-impermeable, amine-reactive reagents is a facile, accessible, and unbiased approach to enrich PM proteins. For unclear reasons however, it results in unexpectedly high contamination with intracellular proteins, reducing its utility. We report that biotinylating human cells with amine-reactive reagents intracellularly labels a small but reproducible population of non-viable cells. Although these dead cells represent only 5±2% of the total, we find that in T cell preparations the dead cells account for 90% of labelled proteins. Depleting Annexin V positive dead T cells post-labelling removes ∼99% of the intracellularly labelled cells, resulting in markedly improved PM identifications, peptide counts, and iBAQ intensities. Correspondingly, we found substantial depletion of intracellular proteins, particular of nuclear origin. Overall, the cumulative intensity of PM proteins increased from 4% to 55.8% with dead cell depletion. Finally, we demonstrate that immature ER/Golgi glycoforms of CD11a and CD18 are selectively removed by dead-cell depletion. We conclude that high intracellular labelling of non-viable cells is the major source of intracellular protein contaminants in amine-reactive surface enrichment methods and can be reduced by dead-cell depletion post-labelling, improving both sensitivity and accuracy of plasma membrane proteomics.