Modeling the separation of small peptides by cation-exchange chromatography

Cation-exchange chromatography was applied for the separation of short synthetic peptide standards, with various charges and hydrophobicities. The methodology to develop simple, reproducible and accurate models, based on physicochemical peptide properties, was described. A multilinear regression method was used for the calculation of the models, and descriptors were chosen according to the observed phenomena. The predictive and interpretative ability of the chromatographic models was evaluated considering cross-validated data (root mean-squared error of calibration, root mean-squared error, root mean-squared error of cross-validation and the Fisher ratio). Hydrophobic coefficients for amino acids were calculated with or without consideration of peptide sequences. A simple model, with only two parameters (charge and hydrophobic coefficient) was built. It enabled an accurate prediction of short peptide elution (up to nine residues). As the model was intended for further characterization of complex mixtures of unknown peptides, some mixtures were analyzed to investigate possible interactions between molecules. Peptides eluted in exactly the same pattern as when injected alone, supporting the use of these models for complex mixtures of small peptides.