Advances in Lipid Analysis/Lipidomics – Analyses of Phospholipids by Recent Application of Mass Spectrometry

  • R. Taguchi
Reference work entry


Mass spectrometry (MS) has become a most useful tool in the analysis of phospholipids. Analysis of molecular species of phospholipids adding to that of their classes and subclasses is necessary to elucidate their physiological functions. As analytical methods for lipidomics, basically three different types of approaches in the identification of phospholipid molecular species can be selected. The first one is shotgun LC-MS/MS analysis with data-dependent scan, the second one is structure-related focused methods such as precursor ion scanning or neutral loss scanning. Both types of data can be subjected to our search engine, “Lipid Search” (, and most probable molecular species can be obtained with their compensated ion intensities. The lipid database for this search engine was constructed theoretically from their structure similarities and variations in polar head groups and fatty carbonyl chains. And identified individual molecular species can be automatically profiling according to their compensated ion intensities. The third method, such as multiple reaction monitoring, is also important for detecting very small amounts of targeted molecules such as lipid mediators or oxidized lipid metabolites. The choice of these three different kinds of methods seems to be very important for neurochemical research for detecting different kinds of lipid metabolites such as unknown lipid ligands, focused class of lipids, or targeted minor lipid mediators.


Molecular Species Multiple Reaction Monitoring Neutral Loss Polar Head Group Fatty Acyl Chain 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

List of Abbreviations:


collision-induced dissociation


electrospray ionization


high-performance liquid chromatography


liquid chromatography


mass spectrometry














ultra performance liquid chromatography



This work was supported by special Coordination fund from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government, and a fund from Core Research for Evolutional and Technology (CREST) of Japan Science and Technology Agency (JST).


  1. Di Paolo G, Moskowitz HS, Gipson K, Wenk MR, Voronov S, Obayashi M, Flavell R, Fitzsimonds RM, Ryan TA, De Camilli P. 2004. Impaired PtdIns(4,5)P2 synthesis in nerve terminals produces defects in synaptic vesicle trafficking. Nature 431: 415-422.PubMedCrossRefGoogle Scholar
  2. Domingues P, Domingues MR, Amado FM, Ferrer- Correia AJ. 2001. Characterization of sodiated glycerol phosphatidylcholine phospholipids by mass spectrometry. Rapid Commun Mass Spectrom 15: 799–804.PubMedCrossRefGoogle Scholar
  3. Ekroos K, Chernushevich LV, Simons K, Shevchenko A. 2002. Quantitative profiling of phospholipids by multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer. Anal Chem 74: 941–949.PubMedCrossRefGoogle Scholar
  4. Ekroos K, Ejsing CS, Bahr U, Karas M, Simons K, et al. 2003. Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation. J Lipid Res 44: 2181–2192.PubMedCrossRefGoogle Scholar
  5. Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH Jr, et al. 2005. A comprehensive classification system for lipids. J Lipid Res 46: 839–861.PubMedCrossRefGoogle Scholar
  6. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64–71.PubMedCrossRefGoogle Scholar
  7. Fridriksson EK, Shipkova PA, Sheets ED, Holowka D, Baird B, et al. 1999. Quantitative analysis of phospholipids in functionally important membrane domains from RBL-2H3 mast cells using tandem high-resolution mass spectrometry. Biochemistry 38: 8056.PubMedCrossRefGoogle Scholar
  8. Han X, Gross RW. 1994. Electrospray ionization mass spectroscopic analysis of human erythrocyte plasma membrane phospholipids. Proc Natl Acad Sci USA 91: 10635–10639.PubMedCrossRefGoogle Scholar
  9. Han X, Gross RW. 2005. Shotgun lipidomics: Electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24: 367–412.PubMedCrossRefGoogle Scholar
  10. Han X, Yang J, Cheng H, Ye H, Gross RW. 2004. Toward fingerprinting cellular lipidomes directly from biological samples by two-dimensional electrospray ionization mass spectrometry. Anal Biochem 330: 317–331.PubMedCrossRefGoogle Scholar
  11. Heller DN, Murphy CM, Cotter RJ, Fenselau C, Uy OM. 1988. Constant neutral loss scanning for the characterization of bacterial phospholipids desorbed by fast atom bombardment. Anal Chem 60: 2787–2791.PubMedCrossRefGoogle Scholar
  12. Houjou T, Yamatani K, Nakanishi H, Imagawa M, T, Shimizu et al. 2004. Rapid and selective identification of molecular species in phosphatidylcholine and sphingomyelin by conditional neutral loss scanning and MS3. Rapid Commun Mass Spectrom 18: 3123–3130.PubMedCrossRefGoogle Scholar
  13. Houjou T, Yamatani K, Nakanishi H, Imagawa M, Shimizu T, et al. 2005. A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 19: 654–666.PubMedCrossRefGoogle Scholar
  14. Hsu FF, Turk J. 2003. Electrospray ionization/tandem quadrupole mass spectrometric studies on phosphatidylcholines: The fragmentation processes. J Am Soc Mass Spectrom 14: 352–363.PubMedCrossRefGoogle Scholar
  15. Ishida M, Imagawa M, Shimizu T, Taguchi R. 2005a. Specific detection of lysophosphatidic acids in serum extracts by tandem mass spectrometry. J Mass Spectrom Soc Jpn 53: 25–32.Google Scholar
  16. Ishida M, Imagawa M, Shimizu T, Taguchi R. 2005b. Effective Extraction and analysis for lysophosphatidic acids and their precursors in human plasma usng electrospray ionization mass spectrometry. J Mass Spectrom Soc Jpn 53: 217–226.Google Scholar
  17. Ishida M, Yamazaki T, Houjou T, Imagawa M, Harada A, et al. 2004. High-resolution analysis by nano-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for the identification of molecular species of phospholipids and their oxidized metabolites. Rapid Commun Mass Spectrom 18: 2486–2494.PubMedCrossRefGoogle Scholar
  18. Ivanova PT, Cerda BA, Horn DM, Cohen JS, McLafferty FW, et al. 2001. Electrospray ionization mass spectrometry analysis of changes in phospholipids in RBL-2H3 mastocytoma cells during degranulation. Proc Natl Acad Sci USA 98: 7152–7157.PubMedCrossRefGoogle Scholar
  19. Jones JJ, Stump MJ, Fleming RC, Lay JO Jr, Wilkins CL. 2003. Investigation of MALDI-TOF and FT-MS techniques for analysis of Escherichia coli whole cells. Anal Chem 75: 1340–1347.PubMedCrossRefGoogle Scholar
  20. Kerwin JL, Tuininga AR, Ericsson LH. 1994. Identification of molecular species of glycerophospholipids and sphingomyelin using electrospray mass spectrometry. J Lipid Res 35: 1102–1114.PubMedGoogle Scholar
  21. Khaselev N, Murphy RC. 2000. Electrospray ionization mass spectrometry of lysoglycerophosphocholine lipid subclasses. J Am Soc Mass Spectrom 11: 283–291.PubMedCrossRefGoogle Scholar
  22. Lehmann WD, Koester M, Erben G, Keppler D. 1997. Characterization and quantification of rat bile phosphatidylcholine by electrospray-tandem mass spectrometry. Anal Biochem 246: 102–110.PubMedCrossRefGoogle Scholar
  23. Marto JA, White FM, Seldomridge S, Marshall AG. 1995. Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 67: 3979–3984.PubMedCrossRefGoogle Scholar
  24. Nor Aliza AR, Bedick JC, Rana RL, Tunaz H, Hoback WW, et al. 2001. Arachidonic and eicosapentaenoic acids in tissues of the firefly, Photinus pyralis (Insecta: Coleoptera). Comp Biochem Physiol A Mol Integr Physiol 128: 251–257.PubMedCrossRefGoogle Scholar
  25. Pulfer M, Murphy RC. 2003. Electrospray mass spectrometry of phospholipids. Mass Spectrom Rev 22: 332–364.PubMedCrossRefGoogle Scholar
  26. Ramanadham S, Hsu FF, Bohrer A, Nowatzke W, Ma Z, et al. 1998. Electrospray ionization mass spectrometric analyses of phospholipids from rat and human pancreatic islets and subcellular membranes: Comparison to other tissues and implications for membrane fusion in insulin exocytosis. Biochemistry 37: 4553–4567.PubMedCrossRefGoogle Scholar
  27. Rugger B, Erben G, Sandhoff R, Wieland FT, Lehmann WD. 1997. Quantitative analysis of biological membrane lipids at the low picomole level by nano-electrospray ionization tandem mass spectrometry. Proc Natl Acad Sci USA 94: 2339–2344.CrossRefGoogle Scholar
  28. Taguchi R, Hayakawa J, Takeuchi Y, Ishida M. 2000. Two-dimensional analysis of phospholipids by capillary liquid chromatography/electrospray ionization mass spectrometry. J Mass Spectrom 35: 953–966.PubMedCrossRefGoogle Scholar
  29. Taguchi R, Houjou T, Nakanishi H, Yamazaki T, Ishida M, et al. 2005. Focused lipidomics by tandem mass spectrometry. J Chromatogr B Anal Technol Biomed Life Sci 823: 26–36.CrossRefGoogle Scholar
  30. Tserng KY, Griffin R. 2003. Quantitation and molecular species determination of diacylglycerols, phosphatidylcholines, ceramides, and sphingomyelins with gas chromatography. Anal Biochem 323: 84–93.PubMedCrossRefGoogle Scholar
  31. Wenk MR, Lucast L, Di Paolo G, Romanelli AJ, Suchy SF, et al. 2003. Phosphoinositide profiling in complex lipid mixtures using electrospray ionization mass spectrometry. Nat Biotechnol 21: 813–817.PubMedCrossRefGoogle Scholar
  32. Yokoyama K, Shimizu F, Setaka M. 2000. Simultaneous separation of lysophospholipids from the total lipid fraction of crude biological samples using two-dimensional thin-layer chromatography. J Lipid Res 41: 142–147.PubMedGoogle Scholar

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© Springer Science+Business Media, LLC 2009

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  • R. Taguchi

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