I understand that the proteins must be separated before visualized by the antibody which requires electrophoresis, but I wonder why a native gel electrophoresis would not be preferred as it seems the antibody would recognize the native protein, not the denatured protein as caused by SDS.  Can someone enlighten me please?  

Thanks!

Native gels are more difficult to run starting from the need of knowing and maintaining charge of the target protein during prep, sensitivity to conformation changes and oligemerization as well as generally lower resolution. So usually you do not do it unless you need it. Moreover, antibodies typically only recognize certain epitopes and denaturing the proteins may actually make them more accessible.