Electrophoretic transport of proteins cross electrochemically oxidized multi-walled carbon nanotube (MWCNT) membranes has been investigated. A small charged protein, lysozyme, was successfully pumped MWCNT membranes by an electric field while rejecting larger of lysozome was reduced by a factor of about 30 in comparison to bulk mobility and consistent with the production for hindered transport. Mobilities between 0.33 and 1.4 x 10(-9) m(2) V-1 s(-1) were observed and are approximately 10-fold faster than comparable ordered nanoporous membranes and consistent with continuum models. For mixtures of BSA and lysozyme, complete rejection of BSA is seen with electrophoretic separations.