Assuming that you have tried to reduce the protein(s) before Western
analysis, heated the sample in the presence of SDS, and still get the
putative aggregated product, try amino acid analysis, N-term analysis,
or C-term analysis. While the results will not prove unequivocally that
they are identical, it should certainly prove the opposite. Another
approach is to perform Ouchterlony immunodiffusion in which the proteins
are in adjacent wells. With a polyclonal antibody, identity will be
indicated when the lines of immunoprecipitation fuse with no "spurs."
Lack of identity will yield "spurs." For further information, any good
immunology book will describe this phenomenon in detail.
