Abstract: In order to optimize two-dimensional liquid chromatographic (2D-LC) columns for highly efficient separation of proteins, several liquid chromatographic columns were investigated and evaluated. Weak anion-exchange (WAX) column was chosen as the first dimension because of its extensive protein separation power. By comparison of different WAX chromatographic columns for human liver protein separation, TSKgel DEAE-5PW column was selected as the first dimension of a 2D-LC system. For the second dimension, ten typical reversed-phase (RP) LC columns (250 mm×4.6 mm, 5 μm, 30 nm) were investigated and evaluated. Their silica based RP stationary phases were butyl (C4), octyl (C8) or octadecyl (C18). To evaluate the retention behavior and non-specific protein adsorption ability of these ten columns, four neutral compounds (uracil, nitrobenzene, naphthalene and fluorene) and three standard proteins (cytochrome C, myoglobin and albumin from chicken egg white) were adopted and separated by RPLC. Meantime, WAX fractions were used to investigate the separation ability of different alkyl-bonded silica stationary phase columns for complex protein samples. By comparison of column separation efficiency, adsorption of intact proteins and sample analysis, Jupiter 300 C4 column was finally employed for its excellent separation ability. Optimization of WAX and RPLC columns offers reliable foundation for the construction of 2D-LC protein separation systems.

Key words: intact protein, multidimensional liquid chromatography, Top-down , proteomics