AutoBlot: deterministic single-cell western blotting reveals proteomic diversity in rare cell populations

Protein abundance and proteoform composition are direct determinants of cellular phenotype, yet both remain difficult to quantify in individual cells from specimens available in limited numbers. Single-cell western blotting (scWB) provides quantitative, molecular-mass-resolved protein measurements but relies on Poisson-limited gravity settling, requiring approximately 10⁶ starting cells while constraining single-cell microwell occupancy to a theoretical maximum of 36.8%. Here, we introduce AutoBlot, an image-guided piezoelectric dispensing approach that deterministically loads individual cells into predefined scWB microwells. AutoBlot achieved approximately 98% single-cell occupancy among targeted microwells while operating from as few as 10,000 starting cells. Across the tested cell concentrations, measured occupancy exceeded Poisson predictions by 31- to 904-fold, and the same dispensing strategy enabled deterministic cell-bead co-loading. We applied AutoBlot to 1,449 cells from seven patient-derived breast organoids generated from histologically normal mammary tissue. Measurements of five lineage-associated proteins revealed donor-to-donor variation, differences associated with germline BRCA1 and menopausal status, and discordance between surface-marker- and cytokeratin-based lineage assignments. AutoBlot also resolved ER-immunoreactive species at approximately 66 and 46 kDa in individual PDO cells. These results establish deterministic cell loading as a strategy for extending molecular-mass-resolved single-cell protein analysis to heterogeneous, cell-limited specimens.