Peptides with less than, say, 50 residues are best run by cation-exchange,
even if they're acidic. If you perform the chromatography at pH 2.8 or so,
then you will have uncharged the Asp- and Glu- residues. The only remaining
charged residues will be the basic ones (unless the peptide is sulfated or
phosphorylated). Thus, all peptides will stick to a good Strong Cation-
Exchange (SCX) material, and will elute more or less in order of increasing
absolute number of basic residues with a salt gradient.
Anion-exchange HPLC works well in many cases, but it's not universal the way
that SCX is. Getting all peptides to stick to an anion-exchanger would
require a pH over 12.5 or so in order to uncharge the Arg- residues.
Going on to proteins: It's possible to separate Human Growth Hormone, which
has Asp- at position 130, from HGH with isoAsp- at 130. Deamidation variants
(e.g., distinguishing Asn from Asp) are even better resolved. It would be
helpful to know what the pI is of your protein, and which residue you're
modifying. Call me if you'd like to discuss this.
Andrew Alpert
PolyLC Inc.
Columbia, MD
tel: 410-992-5400