Quantitative bottom-up shotgun lipidomics relies on molecular species-specific “signature” fragments consistently detectable in MS/MS spectra of analytes and standards. Molecular species of glycerophospholipids are typically quantified using carboxylate fragments of their fatty acid moieties produced by higher-energy collisional dissociation of their molecular anions. However, employing standards whose fatty acids moieties are similar, yet not identical to the target lipids could severely compromise their quantification. We developed a generic and portable fragmentation model implemented in the open-source LipidXte software that harmonizes the abundances of carboxylate anion fragments originating from fatty acid moieties having different sn-1/2 position at the glycerol backbone, length of the hydrocarbon chain, number and location of double bonds. The post-acquisition adjustment enables unbiased absolute (molar) quantification of glycerophospholipid species independent of instrument settings, collision energy, and employed internal standards.
Schuhmann, K. et al. Quantitative Fragmentation Model for Bottom-up Shotgun Lipidomics. Analytical Chemistry (2019)