Opinion Article on Lipidomics: Inherent Challenges of Lipidomic Analysis of Sphingolipids

Overview

Journal Biochim Biophys Acta Mol Cell Biol Lipids

Publisher Elsevier

Specialties Biochemistry
Biophysics
Cell Biology

Date 2017 Feb 6

PMID 28161582

Citations 8

Authors

Alfred H Merrill Jr

M Cameron Sullards

Affiliations

Soon will be listed here.

Abstract

A challenge for sphingolipidomic analysis is the vast number of subspecies, including a large number of isomers-a complication that was even appreciated by the original discoverer of sphingolipids J. L. W. Thudichum (The Chemistry of the Brain, p. x, 1884): "In the course of my researches many unforeseen complications arose, prominent amongst which were those caused by the occurrence of chemical principles having the same atomic or elementary composition, but differing in other chemical, or in physical properties, varieties producing the phenomenon which in chemistry is termed isomerism." Therefore, it is essential to choose the appropriate method(s) for the goal of the analysis, to know the assumptions and limitations of method(s) used, and to temper interpretation of the data accordingly. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.

Citing Articles

Don't Be Surprised When These Surprise You: Some Infrequently Studied Sphingoid Bases, Metabolites, and Factors That Should Be Kept in Mind During Sphingolipidomic Studies.

Merrill Jr A Int J Mol Sci. 2025; 26(2).

PMID: 39859363 PMC: 11765627. DOI: 10.3390/ijms26020650.

Unraveling the complexity of glycosphingolipidome: the key role of mass spectrometry in the structural analysis of glycosphingolipids.

Horejsi K, Holcapek M Anal Bioanal Chem. 2024; 416(25):5403-5421.

PMID: 39138658 PMC: 11427620. DOI: 10.1007/s00216-024-05475-7.

ReTimeML: a retention time predictor that supports the LC-MS/MS analysis of sphingolipids.

Allwright M, Guennewig B, Hoffmann A, Rohleder C, Jieu B, Chung L Sci Rep. 2024; 14(1):4375.

PMID: 38388524 PMC: 10883992. DOI: 10.1038/s41598-024-53860-0.

Characterizing human mesenchymal stromal cells' immune-modulatory potency using targeted lipidomic profiling of sphingolipids.

DeVeaux S, Ogle M, Vyshnya S, Chiappa N, Leitmann B, Rudy R Cytotherapy. 2022; 24(6):608-618.

PMID: 35190267 PMC: 10725732. DOI: 10.1016/j.jcyt.2021.12.009.

Identification of circulating sphingosine kinase-related metabolites for prediction of type 2 diabetes.

Chen Q, Wang W, Xia M, Lu Y, Bian H, Yu C J Transl Med. 2021; 19(1):393.

PMID: 34530846 PMC: 8447705. DOI: 10.1186/s12967-021-03066-z.

References

Liebisch G, Vizcaino J, Kofeler H, Trotzmuller M, Griffiths W, Schmitz G . Shorthand notation for lipid structures derived from mass spectrometry. J Lipid Res. 2013; 54(6):1523-1530. PMC: 3646453. DOI: 10.1194/jlr.M033506. View

Jimenez-Rojo N, Sot J, Busto J, Shaw W, Duan J, Merrill Jr A . Biophysical properties of novel 1-deoxy-(dihydro)ceramides occurring in mammalian cells. Biophys J. 2014; 107(12):2850-2859. PMC: 4269796. DOI: 10.1016/j.bpj.2014.10.010. View

Sullards M, Liu Y, Chen Y, Merrill Jr A . Analysis of mammalian sphingolipids by liquid chromatography tandem mass spectrometry (LC-MS/MS) and tissue imaging mass spectrometry (TIMS). Biochim Biophys Acta. 2011; 1811(11):838-53. PMC: 3205276. DOI: 10.1016/j.bbalip.2011.06.027. View

Russo S, Tidhar R, Futerman A, Cowart L . Myristate-derived d16:0 sphingolipids constitute a cardiac sphingolipid pool with distinct synthetic routes and functional properties. J Biol Chem. 2013; 288(19):13397-409. PMC: 3650378. DOI: 10.1074/jbc.M112.428185. View

Kliman M, May J, McLean J . Lipid analysis and lipidomics by structurally selective ion mobility-mass spectrometry. Biochim Biophys Acta. 2011; 1811(11):935-45. PMC: 3326421. DOI: 10.1016/j.bbalip.2011.05.016. View

Ladisch S, Gillard B . A solvent partition method for microscale ganglioside purification. Anal Biochem. 1985; 146(1):220-31. DOI: 10.1016/0003-2697(85)90419-1. View

Quehenberger O, Armando A, Brown A, Milne S, Myers D, Merrill A . Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 2010; 51(11):3299-305. PMC: 2952570. DOI: 10.1194/jlr.M009449. View

Wang M, Han X . Multidimensional mass spectrometry-based shotgun lipidomics. Methods Mol Biol. 2014; 1198:203-20. PMC: 4261229. DOI: 10.1007/978-1-4939-1258-2_13. View

Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T . Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res. 2008; 50 Suppl:S9-14. PMC: 2674711. DOI: 10.1194/jlr.R800095-JLR200. View

10.

Sims K, Tytler E, Tipton J, Hill K, Burgess S, Shaw W . Avanti lipid tools: connecting lipids, technology, and cell biology. Biochim Biophys Acta. 2014; 1841(8):1038-48. DOI: 10.1016/j.bbalip.2014.05.008. View

11.

Woods A, Jackson S . The application and potential of ion mobility mass spectrometry in imaging MS with a focus on lipids. Methods Mol Biol. 2010; 656:99-111. PMC: 2953758. DOI: 10.1007/978-1-60761-746-4_5. View

12.

Lydic T, Busik J, Reid G . A monophasic extraction strategy for the simultaneous lipidome analysis of polar and nonpolar retina lipids. J Lipid Res. 2014; 55(8):1797-809. PMC: 4109773. DOI: 10.1194/jlr.D050302. View

13.

Shaner R, Allegood J, Park H, Wang E, Kelly S, Haynes C . Quantitative analysis of sphingolipids for lipidomics using triple quadrupole and quadrupole linear ion trap mass spectrometers. J Lipid Res. 2008; 50(8):1692-707. PMC: 2724058. DOI: 10.1194/jlr.D800051-JLR200. View

14.

Merrill Jr A . Sphingolipid and glycosphingolipid metabolic pathways in the era of sphingolipidomics. Chem Rev. 2011; 111(10):6387-422. PMC: 3191729. DOI: 10.1021/cr2002917. View

15.

Birkholz A, Howell A, Kronenberg M . The alpha and omega of galactosylceramides in T cell immune function. J Biol Chem. 2015; 290(34):20746. PMC: 4543636. DOI: 10.1074/jbc.A115.647057. View

16.

Fahy E, Sud M, Cotter D, Subramaniam S . LIPID MAPS online tools for lipid research. Nucleic Acids Res. 2007; 35(Web Server issue):W606-12. PMC: 1933166. DOI: 10.1093/nar/gkm324. View

17.

Farwanah H, Kolter T . Lipidomics of glycosphingolipids. Metabolites. 2014; 2(1):134-64. PMC: 3901200. DOI: 10.3390/metabo2010134. View

18.

van Echten-Deckert G . Sphingolipid extraction and analysis by thin-layer chromatography. Methods Enzymol. 2000; 312:64-79. DOI: 10.1016/s0076-6879(00)12900-3. View

19.

Parry S, Ledger V, Tissot B, Haslam S, Scott J, Morris H . Integrated mass spectrometric strategy for characterizing the glycans from glycosphingolipids and glycoproteins: direct identification of sialyl Le(x) in mice. Glycobiology. 2007; 17(6):646-54. DOI: 10.1093/glycob/cwm024. View

20.

Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes R, Cotter D . Bioinformatics and systems biology of the lipidome. Chem Rev. 2011; 111(10):6452-90. PMC: 3383319. DOI: 10.1021/cr200295k. View