Ed Rybicki recently suggested agarose gel electrophoresis as a
method to separate different particles within a given preparation.
Another strong contended is using isoelectric focusing in agarose
gels. Using non-ionic or zwitterionic detergents, presuming they're needed
at all, can be used to prevent aggregation without altering pI values.
I can provide methodology and precedent for this technique if the original
inquirer wishes.