I agree with DK, hydrophobic interaction might be the best solution, it
might have very high resolution for different folding forms. But it needs to
be specifically optimised for every protein....
1) what about native IEF ? - but it too can not be used for every protein -
many will precipitate.
2) also, if you are working with small proteins stabilised by disulfides,
may be HPLC will help
may be it would be better just to use the native host, and expressing the
tagged proteins in it ?