Recent experimental studies have demonstrated that membrane systems can be used to separate protein variants that differ by only a single amino acid residue, although the selectivity and purification factor were relatively low. The objective of this study was to examine theoretically the effects of the membrane surface charge density and pore size distribution on the separation of protein variants by high performance tangential flow filtration. Model calculations based on the partitioning of a charged sphere into a charged cylindrical pore, including a shift in pH within the pores due to preferential partitioning of the positive hydrogen ions, are in good agreement with literature data for the separation of myoglobin and a succinylated variant. Significantly greater selectivity was obtained by reducing the mean pore size and increasing the membrane surface charge density, both of which enhance the electrostatic interactions arising from the small charge difference between the native protein and the variant. Purification factor-yield plots were developed to evaluate the separation performance. Proper selection of membrane properties gave 100-fold purification at 90% product yield for the separation of variants differing at only a single lysine group. (C) 2004 Elsevier B.V. All rights reserved.