gel chromatography only separates on size and shape of the molecule. There may be many proteins of similar size and shape in a peak but these can then separate when the separation method relies on the electric charge on the outside of the protein due to different amino acids being on the outside of the molecules

More detail needed.

What sample were you running on the size exclusioni chromatography?  The single peak could have consitituted a multi-protein complex or a number of polypepitdes joined by cysteine bridges.  (was your PAGE gel denaturing?)

gel chromatography only separates on size and shape of the molecule. There may be many proteins of similar size and shape in a peak but these can then separate when the separation method relies on the electric charge on the outside of the protein due to different amino acids being on the outside of the molecules

yes Marcus Hanley, I used SDS PAGE gel. my sample was protein belongs to drosophila which I isolated using bacterial system

 Thank you Paul Rutland