Peptide retention time prediction for immobilized artificial membrane phosphatidylcholine stationary phase: Method development and preliminary observations

Abstract

Development of the first peptide retention prediction model for immobilized artificial membrane phosphatidylcholine (IAM.PC) stationary phase is reported. 2D liquid chromatography coupled to tandem mass spectrometry (2D LC-MS/MS) analysis of a whole cell lysate of S. cerevisiae yielded a retention dataset of ~29,500 tryptic peptides; sufficient for confident assignment of retention coefficients which determine the contribution of individual amino acids in peptide retention. Retention data from the first dimension was used for the modelling: an IAM.PC.DD2 column, with pH 7.4 ammonium bicarbonate, and a water/acetonitrile gradient. Peptide separation using the IAM.PC.DD2 phase was compared to a standard C18 phase (Luna C18(2)). There was a significant reduction in peptide retention (~14 % acetonitrile on average), indicating that the phosphatidylcholine stationary phase is significantly more hydrophilic. In comparison to the C18 phase, a substantial increase was found in the relative retention contribution for the positively charged Arg and Lys, and the aromatic Tyr, Trp and His residues. A decrease in retention contribution was observed for the negatively charged Asp and Glu. This indicates an involvement of electrostatic interactions with the glycerophosphate functional groups, and possibly, delocalization effects from hydrogen bonds between the phosphate group and the aromatic side chains in the separation mechanism.