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Anal Chem. 2019 Sep 17;91(18):12085-12093. doi: 10.1021/acs.analchem.9b03270. Epub 2019 Sep 5.

Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics.

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Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstr. 108 , 01307 Dresden , Germany.
Department of Nephrology and Hypertension , Inselspital, Bern University Hospital , Freiburgstr. 15 , 3010 Bern , Switzerland.
Department for BioMedical Research , University of Bern , Murtenstr. 35 , 3010 Bern , Switzerland.
Thermo Fisher Scientific , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany.


Quantitative bottom-up shotgun lipidomics relies on molecular species-specific "signature" fragments consistently detectable in tandem mass 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 positions at the glycerol backbone, length of the hydrocarbon chain, and number and location of double bonds. The postacquisition adjustment enables unbiased absolute (molar) quantification of glycerophospholipid species independent of instrument settings, collision energy, and employed internal standards.

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