We have developed a novel microfluidic droplet based assay for analysis of low expressed cell surface proteins on individual cells at rates of hundreds of cells/s by antibody coupled enzymatic amplification in monodisperse droplets [1]. Here we expand the method to include concurrent analysis of multiple populations of single cells. We report the validation of the method by analyzing the human monocytic cell line U937 for two low expressed markers, CCR5 and CD19. Comparing our method to standard flow cytometry, we demonstrate increased peak separation, which should allow sorting by these low expressed biomarkers unavailable to flow cytometry.