The fluxes of bovine serum albumin and bovine hemoglobin through charged nanopores inside polymeric membranes are measured and analysed as a function of the pore size, the applied voltage to the nanopore surface, the solution ionic strength and pH. The pore surface has been modified by a self-assembled monolayer. The electrostatic interaction of the protein with the nanopore surface gives low transport rates except at the protein's isoelectric point and the minimum of the effective, voltage-induced nanopore charge. The electrostatic sieving effect allows for the separation of proteins with similar molecular weights.