The use of ordered mesoporous materials for protein separations is relatively new. We have previously reported on the synthesis of spherical SBA-15 type ordered materials for chromatographic bioseparations. Spherical particles suitable for chromatography have been synthesized, and have been used to show size-based protein separations. However, the measurement technique (adsorption isotherms) used for obtaining protein capacity in these materials did not conclusively show them to be sharply size selective. In this paper we report on the use of two complementary techniques to confirm the size-selective separation of proteins on mesoporous SBA-15 materials. Confocal Scanning Laser Microscopy (CSLM) has been used to visualize the separation, while Flow Micro Calorimeter (FMC) was used to measure the energetics during the adsorption process. FMC results show that protein adsorption inside the pores results in large heats of adsorption, relative to that from external adsorption; these results will be shown to correspond correctly with CSLM protein imaging data. The pores of the size-selective SBA-15 have also been functionalized with the sulfonate ligand, to give a size-selective anion exchanger (dual-mode separation media) for protein purifications. Studies with probe proteins on this material have shown that protein uptake can be precisely tuned using a combination pore size and solution pH. For example, large-pore SBA-15 (pore size ~21 nm) at pH 4 has a very high capacity for BSA (pI = 4.8; size: 4 nm * 4 nm *14 nm) of ~600 mg/g, and at pH 8 very low loading (30 mg/g) is observed. Moreover, a small pore-size sulfonate SBA-15 (~8 nm) has no capacity for BSA at pH 4. The implications of these results in enhancing selectivity and efficiency in chromatographic bioseparations will be discussed.