Abstract
Electrospray ionization mass spectrometry has revolutionized the way lipids are studied. In this work, we present a tutorial for analyzing class-specific lipid spectra obtained from a triple quadrupole mass spectrometer. The open-source software MZmine 2.21 is used, coupled with LIPID MAPS databases. Here, we describe the steps for lipid identification, ratiometric quantification, and briefly address the differences to the analyses when using direct infusion versus tandem liquid chromatography–mass spectrometry (LC–MS). We also provide a tutorial and equations for quantification of lipid amounts using synthetic lipid standards and normalization to a protein amount.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Han X, Yang K, Gross RW (2012) Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses. Mass Spectrom Rev 31(1):134–178. doi:10.1002/mas.20342
Shevchenko A, Simons K (2010) Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol 11(8):593–598. doi:10.1038/nrm2934
Hannun YA, Obeid LM (2008) Principles of bioactive lipid signalling: lessons from sphingolipids. Nat Rev Mol Cell Biol 9(2):139–150. doi:10.1038/nrm2329
Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37(8):911–917. doi:10.1139/o59-099
Bhattacharya SK (2013) Recent advances in shotgun lipidomics and their implication for vision research and ophthalmology. Curr Eye Res 38(4):417–427. doi:10.3109/02713683.2012.760742
Fahy E, Sud M, Cotter D, Subramaniam S (2007) LIPID MAPS online tools for lipid research. Nucleic Acids Res 35(Web Server issue):W606–W612. doi:10.1093/nar/gkm324
Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res 35(Database issue):D527–D532. doi:10.1093/nar/gkl838
Katajamaa M, Miettinen J, Oresic M (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22(5):634–636. doi:10.1093/bioinformatics/btk039
Pluskal T, Castillo S, Villar-Briones A, Oresic M (2010) MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11:395. doi:10.1186/1471-2105-11-395
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Ma, J., Arbelo, U., Guerra, Y., Aribindi, K., Bhattacharya, S.K., Pelaez, D. (2017). Bioinformatics Pertinent to Lipid Analysis in Biological Samples. In: Bhattacharya, S. (eds) Lipidomics. Methods in Molecular Biology, vol 1609. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6996-8_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6996-8_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6995-1
Online ISBN: 978-1-4939-6996-8
eBook Packages: Springer Protocols