In protein chromatography large molecules have to diffuse into the stationary phase. The molecular sizes of the proteins make the diffusion rates low or very low and the separation can be assumed to be mass transfer limited. In this study three different prepacked columns, with different bead sizes, are used for the separation of IgG and BSA to confirm or reject this assumption in an ion-exchange application. The separations are modeled and calibrated against gradient elution data. Model calibration of reaction-dispersive, transport-dispersive and general rate model structures are discussed and the analysis shows that the columns are best modeled by different model structures, because different behaviors are rate-limiting. Experiments call be described surprisingly well by reaction-dispersive model structures, especially for BSA. Broad elution peaks for IgG indicate mass transfer limitations. Calibration of models capturing diffusive effects shows that the pore diffusion coefficients are much higher than expected, compared with the literature, indicating that there are other forces dominating the mass transport in the beads.