This article is available online at http://www.jlr.org an orthogonal separation to LC/ESI/MS/MS for quantifying isomeric cerebrosides in plasma and cerebrospinal fluid. J. Lipid Res. 2019. 60: 200-211.Supplementary key words lipidomics • liquid chromatography • mass spectrometry • tandem mass spectrometry • electrospray ionization • cerebrosides • sphingolipids • differential ion mobility spectrometry Glycosphingolipids (GSLs) are essential plasma membrane lipid components of eukaryotes. Together with cholesterol and sphingomyelin, GSLs form microdomains on plasma membranes that play important roles in various cellular activities such as adhesion, growth, and differentiation (1). The simplest GSLs are monohexosylceramides (also known as cerebrosides). Cerebrosides are composed of a lipid, ceramide, that is embedded in the outer leaflet of the plasma membrane, and a sugar moiety, either glucose Abstract Cerebrosides, including glucosylceramides (GlcCers) and galactosylceramides (GalCers), are important membrane components of animal cells with deficiencies resulting in devastating lysosomal storage disorders. Their quantification is essential for disease diagnosis and a better understanding of disease mechanisms. The simultaneous quantification of GlcCer and GalCer isomers is, however, particularly challenging due to their virtually identical structures. To address this challenge, we developed a new LC/ MS-based method using differential ion mobility spectrometry (DMS) capable of rapidly and reproducibly separating and quantifying isomeric cerebrosides in a single run. We show that this LC/ESI/DMS/MS/MS method exhibits robust quantitative performance within an analyte concentration range of 2.8-355 nM. We further report the simultaneous quantification of nine GlcCers (16:0, 18:0, 20:0, 22:0, 23:0, 24:1, 24:0, 25:0, and 26:0) and five GalCers (16:0, 22:0, 23:0, 24:1, and 24:0) molecular species in human plasma, as well as six GalCers (18:0, 22:0, 23:0, 24:1, 24:0 and 25:0) and two GlcCers (24:1 and 24:0) in human cerebrospinal fluid. Our method expands the potential of DMS technology in the field of glycosphingolipid analysis for both biomarker discovery and drug screening by enabling the unambiguous assignment and quantification of cerebroside lipid species in biological samples