Highly multiplexed and quantitative cell surface protein profiling using genetically barcoded antibodies

Next generation sequencing (NGS) allows for sensitive quantification of DNA and RNA. It would be highly desirable to have a systematic equivalent for assaying cellular protein levels on living cells. We present a highly multiplexed, quantitative, and inexpensive sequencing-based proteomic method using genetically barcoded antibodies called Phage-antibody Next Generation Sequencing (PhaNGS). We demonstrate the utility of PhaNGS by showing how a set of 144 targeted Fab-phage can reliably detect changes in 44 targeted cell surface proteins in drug sensitive and resistant B-cells, or upon induction of the Myc oncogene. We examined profiling of Fab-phage against parental and surface GFP over-expression conditions with 2 replicates each for HeLa cells; we examined diagnosis and relapse conditions with 4 replicates each for LAX7 cells; we examined induction of expression or control conditions with 3 replicates each in surface-CDCP1-expressing T-REx cells; we examined control (MycON), MycOFF, and wash-out (MycBACKON) conditions with 4 replicates each for P493-6 cells; we examined 72 single T-REx cells over-expressing surface GFP; and we examined 95 single P493-6 cells. Each individual group comes with an input mixture against which the outputs are compared.