Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all of these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE ensures duty-cycle time for analyzing prioritized peptides across all single cells (thus increasing data consistency) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth. These strategies increased the quantified data points for challenging peptides and the overall proteome coverage about 2-fold. pSCoPE enabled quantifying proteome polarization in primary mouse macrophages and linking it to phenotypic variability in endocytic activity. Proteins annotated to phagosome maturation and proton transport showed concerted variation for both untreated and lipopolysaccharide-treated macrophages, indicating a conserved axis of polarization. pSCoPE further quantified proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is easily accessible and likely to benefit many applications, especially mechanistic analysis seeking to focus on proteins of interest without sacrificing proteome coverage. ### Competing Interest Statement The authors have declared no competing interest.