Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

Gerhard Liebisch¹, Eoin Fahy², Junken Aoki³, Edward A Dennis⁴, Thierry Durand⁵, Christer S Ejsing⁶, Maria Fedorova⁷, Ivo Feussner⁸, William J Griffiths⁹, Harald Köfeler¹⁰, Alfred H Merrill Jr¹¹, Robert C Murphy¹², Valerie B O'Donnell¹³, Olga Oskolkova¹⁴, Shankar Subramaniam¹⁵, Michael J O Wakelam¹⁶, Friedrich Spener¹⁷

Affiliations

¹ Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
² Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
³ Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
⁴ Department of Chemistry and Biochemistry, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
⁵ Institute of Biomolecules Max Mousseron, University of Montpellier, CNRS, ENSCM, Montpellier, France.
⁶ Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁷ Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany.
⁸ Department of Plant Biochemistry, Albrecht-von-Haller-Institute and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany.
⁹ Swansea University Medical School, Swansea, United Kingdom.
¹⁰ Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria.
¹¹ School of Biological Sciences and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
¹² Department of Pharmacology, University of Colorado at Denver, Aurora, CO, USA.
¹³ Systems Immunity Institute, Cardiff University, Cardiff, United Kingdom.
¹⁴ Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria.
¹⁵ Department of Biomedical Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
¹⁶ Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
¹⁷ Department of Molecular Biosciences, University of Graz, Graz, Austria; Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria. Electronic address: fritz.spener@uni-graz.at.

PMID: 33037133
PMCID: PMC7707175
DOI: 10.1194/jlr.S120001025

Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

Gerhard Liebisch et al. J Lipid Res. 2020 Dec.

. 2020 Dec;61(12):1539-1555.

doi: 10.1194/jlr.S120001025. Epub 2020 Oct 9.

Authors

Affiliations

¹ Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
² Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
³ Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
⁴ Department of Chemistry and Biochemistry, Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
⁵ Institute of Biomolecules Max Mousseron, University of Montpellier, CNRS, ENSCM, Montpellier, France.
⁶ Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁷ Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany.
⁸ Department of Plant Biochemistry, Albrecht-von-Haller-Institute and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, Germany.
⁹ Swansea University Medical School, Swansea, United Kingdom.
¹⁰ Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria.
¹¹ School of Biological Sciences and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
¹² Department of Pharmacology, University of Colorado at Denver, Aurora, CO, USA.
¹³ Systems Immunity Institute, Cardiff University, Cardiff, United Kingdom.
¹⁴ Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria.
¹⁵ Department of Biomedical Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
¹⁶ Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
¹⁷ Department of Molecular Biosciences, University of Graz, Graz, Austria; Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria. Electronic address: fritz.spener@uni-graz.at.

PMID: 33037133
PMCID: PMC7707175
DOI: 10.1194/jlr.S120001025

Abstract

A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation.

Keywords: fatty acyls; glycerolipids; glycerophospholipids; lipidomics; mass spectrometry; sphingolipids; sterols.

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Conflict of interest statement

Conflict of interest—The authors declare that they have no conflicts of interest with the contents of this article.

Figures

**Fig. 1.**
Hierarchical scheme for the analysis of glucosylceramide. “Analysis” presents MS-data and “Annotation” the respective hierarchical *levels* with corresponding shorthand annotation. The chemical structure illustrates the *Complete Structure level*, numbers along the sphingoid base indicate conventional numbering of carbons therein.

See this image and copyright information in PMC

References

1. O’Donnell V. B., Dennis E. A., Wakelam M. J. O., and Subramaniam S.. 2019. LIPID MAPS: serving the next generation of lipid researchers with tools, resources, data, and training. Sci. Signal. 12: eaaw2964. - PubMed
1. Fahy E., Subramaniam S., Brown H. A., Glass C. K., Merrill A. H. Jr., Murphy R. C., Raetz C. R., Russell D. W., Seyama Y., Shaw W., et al. . 2005. A comprehensive classification system for lipids. J. Lipid Res. 46: 839–861. - PubMed
1. Fahy E., Subramaniam S., Murphy R. C., Nishijima M., Raetz C. R., Shimizu T., Spener F., van Meer G., Wakelam M. J., and Dennis E. A.. 2009. Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. 50 (Suppl.): S9–S14. - PMC - PubMed
1. Liebisch G., Vizcaino J. A., Köfeler H., Trötzmüller M., Griffiths W. J., Schmitz G., Spener F., and Wakelam M. J.. 2013. Shorthand notation for lipid structures derived from mass spectrometry. J. Lipid Res. 54: 1523–1530. - PMC - PubMed
1. Ekroos K. 2012. From molecular lipidomics to validated clinical diagnosis. In Lipidomics: Technologies and Applications. K. Ekroos, editor. Wiley-VCH, Weinheim, Germany. 1–16.

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Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

Affiliations

Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

Authors

Affiliations

Abstract

Conflict of interest statement

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References

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