Prediction of Peptide Retention in RP-LC

The retention of small peptides can be predicted by summing the hydrophobic contribution to retention of each amino acid of peptides. But the retention time of peptides larger than 10–15 residues are less than that predicted by summing the retention coefficients of each constitutive residue. A new prediction model, considering the effects of the peptide length and contact area of each amino acid with the stationary phase for larger peptides was proposed. The model was validated by 136 peptides identified by nano-flow 2-D-LC-ESI-MS-MS platform and other retention data observed from literature. The high degree of correlation between the observed and predicted retention time by using the new model is not only good evidence for the accuracy of our predictive method, but supports the supposition that the peptide length and contact area of each amino acid with stationary phase are important factors affecting peptide retention time for larger peptide. In addition it is found that the range of peptide length is wider, the accuracy of prediction is better. The ratio coefficient of surface area of non-polar, polar and charged amino residues contacting with the stationary phase were all calculated to be less than one.