Beyond Molecular Weight: Peptide Characteristics Influencing the Sensitivity of Retention to Changes in Organic Solvent in Reversed-Phase Chromatography

The <i>S</i> value, representing the sensitivity of peptide retention to changes in organic solvent concentrations in reversed-phase liquid chromatography (RP-LC), is a critical parameter for optimizing gradient elution and enhancing separation selectivity. While the influence of molecular weight on <i>S</i> values is well-documented, the contribution of other peptide-specific characteristics remains insufficiently understood. This study experimentally evaluated a structurally diverse dataset of 18 peptides and applied a multifaceted data approach combining partial least squares, Kendall's tau correlation analysis, and machine learning models (multiple linear regression, decision tree, and lasso) to identify key molecular features affecting the <i>S</i> value. Factors such as hydrophobicity and the number of CH₂R₂ groups, structural flexibility, isoelectric point, and the number of lysine residues emerged as significant contributors. A predictive model was developed, offering a tool for method optimization in peptide separations.