Will it dissolve in 85% acetonitrile or PrOH? If so, then you can use
Hydrophilic Interaction Chromatography (HILIC) (@ J. Chromatogr. 499 (1990)
177). Is your objective to resolve the homologous series representing the
failure sequences? HILIC should work pretty well for this; Ala is reasonably
well-retained in HILIC, and the absence of an Ala residue should permit decent
separation from the complete peptide. How many Ala residues are in the target
sequence?
Regards,
Andy Alpert
PolyLC Inc.
Columbia, MD
tel: 410-992-5400 e-mail: PolyLC@aol.com