Unfortunately with such small details it is hard to comment, there are dozens of biophysical techniques. If you just want to figure out vials and If those two varients have different tag ( for example strp and his tag ) then just do the western blot

You can use intact protein mass spectrometry to get an exact mass of each protein to compare to the known masses. A well-calibrated instrument should be able to get within a few Da of the correct mass if there are no uncharacterized post-translational modifications. You will have to find a facility that has the equipment for this, but it is fast and can be done with very little protein.

If the masses of the two proteins are identical but the sequences are different (e.g. leucine changed to isoleucine), then sequencing by mass spectrometry may be the only way to tell them apart.

Another idea is to run an isoelectric focusing gel, which would distinguish the proteins based on their isoelectric points (pI). Of course, you need a standard of comparison. Even a single charged amino acid difference could be enough to change the pI, although changes in uncharged residues may not have any effect on pI.

Hi,

another interesting technique is Ion Mobility Spectrometry-Mass Spectrometry as it can separate isomers if their shape is different.

Thanks you all for your valuable suggestions...

I hope I could be able to solved my problems sooner or later.

Isoelectric points may be different enough to facilitate identification by isoelectric focusing (2D gel), depending on the nature of the mutations.