Peptide retention time prediction for hydrophilic interaction liquid chromatography at acidic pH in formic-acid based eluents.

• Peptide separation selectivity have been evaluated for ZIC-HILIC, XBridge Amide, ZIC-cHILIC columns at acidic pH using ∼30,000 peptides datasets. • Peptide retention at pH 2.7 HILIC increases in order of ZIC-cHILIC < XBridge amide < ZIC-HILIC. • Composition and sequence-dependent retention factors contributing to peptide retention on HILIC at acidic pH have been elucidated. • The peptide separation orthogonality for HILIC-RPLC 2D LC combinations was found higher at pH 4.5 compared to pH 2.7. Peptide separation selectivity was evaluated for hydrophilic interaction liquid chromatography (HILIC) ZIC-HILIC, ZIC-cHILIC, and XBridge Amide sorbents using formic acid as eluent additive (pH 2.7). Sequence-specific retention prediction algorithms were trained using retention datasets of ∼30,000 peptides for each column. Our retention models were able to attain ∼0.98 R2-value and yielded retention coefficients that can be probed to understand peptide-stationary phase interaction. Overall, the hydrophilicity for these columns decreased when the mobile phase changed pH from 4.5 to 2.7, when using 0.1 % formic acid in the mobile phase. The acidic residues became protonated, and the resultant hydrophilic interaction is dampened at the lower pH, leaving only the basic residues as the primary hydrophilic interactors. Hence, peptides of increasing charge have higher retention. In this comparison between the three columns, ZIC-HILIC has the highest chromatographic resolution between groups of peptides of different charge. From the position-dependent retention coefficients for ZIC-HILIC at pH 2.7, we found that the amino acids at the terminal positions of the peptide modulate the basicity of the N-terminal amino group or the C-terminal Arg/Lys for tryptic peptides. With respect to the separation orthogonality between HILIC and acidic pH RPLC for two dimensional separations, the orthogonality values were lower at pH 2.7 than operating HILIC at pH 4.5 for the first dimension. We also demonstrate that ZIC-HILIC was able to distinguish citrullinated and deamidated peptides based on predicted retention values. [ABSTRACT FROM AUTHOR]