High Binding Capacity. While agarose beads may have a porous center which significantly increases their binding capacity, magnetic beads are significantly smaller than agarose beads (1 to 4μm). This gives them an effective surface area-to-volume ratio for optimum antibody binding. In addition, magnetic beads can aggregate without the need for centrifugation, thereby increasing the yield of delicately attached protein complexes.
Reduced Antibody Consumption. Since agarose beads are porous and have high binding capacity, they require larger amounts of antibodies to produce accurate results. The antibody can be trapped inside the bead and fail to properly bind the protein of interest. When this happens, you may need to use more antibody. You wouldn't have this problem with magnetic beads since they are non-porous and antibody binding is limited to the outer surface of the bead.
Keep in mind that when the amount of antibody available for the immunoprecipitation experiment is less than sufficient to saturate the agarose beads, you can end up with particles that are only partially coated with antibodies. This can be a problem since the unsaturated portion of the beads will then be free to bind with anything that will stick. In such cases, you can expect elevated background signal due to non-specific binding of lysate components to the beads.
Reduced Sample Loss. Since magnetic beads do not require centrifugation, there is no risk of aspirating immune complexes that are bounded to the beads. This also reduces the risk of breaking weak antibody-antigen binding and the subsequent loss of target protein for a more accurate quantitation of your protein of interest and better reproducibility.
