NMR and x-ray crystallography are normally used for protein structure determination, but both techniques has limitations (well of course) and think one as simple as size could be the answer, but I am no expert at all, I have friend though who is deeply involved in nuclear magnetic resonance (NMR) (he even got a price for it ). But is a very nice technique, but also hard to really grasp the total understanding of...
But I see what what u mean about specie separation, might not really be present/measurable on a this kind of detail level so ur more working on the division level, sounds more feasible as well!!! Well again I wish u luck!
(I will soon (when I have them taken) share some confocal imaging I have been working on for my master thesis in my picture thread, I hope whey will end up looking good, should be a tad "psychedelic" )