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There is little evidence that reversed-phase high-performance liquid chromatography can be successfully used in the analysis of protected peptide segments. The use of C18 and CN packings and mobile phases containing water-acetonitrile with or without propionic acid in the separation of complex mixtures of synthetic protected peptides is reported. CN packings show a lower efficiency and exhibit poorer resolution than C18 packings but provide different separations. The addition of propionic acid to the mobile phase increases the retention time of peptides but also provides dramatic and useful changes in selectivity. Retention is not related to the molecular mass of the protected peptides but mainly to their hydrophobicity.
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