Ion Pair Liquid Chromatography–Mass Spectrometry for Probing the Polar Metabolome

Abstract

Ion pair liquid chromatography (IP-LC) is a variant of reversed-phase liquid chromatography, which achieves the retention and separation of charged or ionic compounds on traditional reversed-phase hydrophobic stationary phases by addition of ion pair reagents in the mobile phase. Many metabolites involved in the important anabolic and catabolic metabolic pathways are highly polar and often ionized. IP-LC coupled with tandem mass spectrometry (MS/MS) or high-resolution mass spectrometry (MS) is particularly useful for the analysis of these polar and charged metabolites. In this chapter, we provide an overview on the basics of IP-LC–MS in terms of retention mechanism, critical parameters, and mass spectrometry detection. In addition, we discuss IP-LC–MS based metabolomics with the focus on sample preparation, chromatographic and mass spectrometry methods, as well as potential pitfalls and key solutions. Overall, this review intends to provide a practical framework and guidance for carrying out robust IP-LC–MS based metabolomics.