Evaluation of hydrophilic interaction chromatography (HILIC) versus C₁₈ reversed-phase chromatography for targeted quantification of peptides by mass spectrometry.

Hydrophilic-interaction liquid chromatography (HILIC) is a widely used technique for small polar molecule analysis and offers the advantage of improved sensitivity in mass spectrometry. Although HILIC is today frequently employed as an orthogonal fractionation method for peptides during the proteomic discovery phase, it is still seldom considered for quantification. In this study, the performances in terms of peak capacity and sensitivity of 3 HILIC columns were compared to traditional reversed phase liquid C(18) column in the context of targeted quantification of proteotypic peptides using selected reaction monitoring mode (SRM). The results showed that the maximum sensitivity in HILIC chromatography was achieved by using an amide column without salt buffer and that the signal increased compared to classic reversed phase chromatography. However, the intensity improvement is quite low compared to the one obtained for small molecules. This is due on one hand to a higher matrix effect in HILIC and on the other hand to a change of charge states of peptides in organic solvent (doubly charged to monocharged). The doubly charged ions can be more readily dissociated than singly charged ions, making them ideal for SRM peptide quantification. As a result "supercharging" reagents are added to the mobile phase to shift from predominant singly charged ions to the more favorable doubly charged species. Using such optimized conditions, peptide signal is improved by a factor of between two and ten for 88% of the peptides of the 81 peptides investigated.