Capillary electrophoresis of cationic random coil peptide standards: Effect of anionic ion‐pairing reagents and comparison with reversed‐phase chromatography

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Abstract
The present study compares a charge/hydrophobicity capillary electrophoresis (CE) approach to reversed‐phase high‐performance liquid chromatography (RP‐HPLC) for the separation of three series of four synthetic, random coil peptide standards. Each series has peptides of the same positive charge (+1, +2 and +3 series) and length but differing in hydrophobicity. Complete resolution of the 12 peptides was achieved via a novel CE approach: a capillary zone electrophoresis (CZE) mode effected a separation of identically charged peptides; within each charged group of peptides, the addition of perfluorinated acid anionic ion‐pairing reagents allowed resolution of the peptides through a mechanism based on peptide hydrophobicity which we have termed ioninteraction (II)‐CZE. The peak capacity and peptide resolution of this CE approach was superior to that of RP‐HPLC and stresses an important role for CE for peptide/proteomic applications.

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