Abstract
In recent years, multiple mass-spectrometric methods have been developed to tackle fundamental analytical questions in the field of biology and biochemistry. One essential approach relies on the use of liquid chromatography (LC), for efficient compound separation, coupled to high-resolution mass spectrometry (HR-MS). Even though these techniques are highly sensitive allowing for the reliable measurement of several thousand mass features, the major bottleneck is to convert the measured masses into annotated lipid species. To overcome this problem, we present a simple, example-based workflow, which provides an introduction to basic strategies for the manual validation of LC-MS-based lipidomic data. The whole strategy makes use of a data-independent acquisition (DIA) method, where alternating MS measurement cycles using high and low-energy scans are used. This measurement strategy allows to reliably annotate lipids, based on the exact mass measurements of intact, but also fragmented lipids from continuously recorded spectra.
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References
Muro E, Atilla-Gokcumen GE, Eggert US (2014) Lipids in cell biology: how can we understand them better? Mol Biol Cell 25:1819–1823
Fahy E, Subramaniam S, Brown HA et al (2005) A comprehensive classification system for lipids. J Lipid Res 46:839–861
Fahy E, Subramaniam S, Murphy RC et al (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res 50(Suppl):S9–14
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
Hummel J, Segu S, Li Y et al (2011) Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. Front Plant Sci 2:54
Wenk MR (2005) The emerging field of lipidomics. Nat Rev Drug Discov 4:594–610
Fenn JB, Mann M, Meng CK et al (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71
Blanksby SJ, Mitchell TW (2010) Advances in mass spectrometry for lipidomics. Ann Rev Anal Chem 3:433–465
Harkewicz R, Dennis EA (2011) Applications of mass spectrometry to lipids and membranes. Ann Rev Biochem 80:301–325
Shiva S, Vu HS, Roth MR et al (2013) Lipidomic analysis of plant membrane lipids by direct infusion tandem mass spectrometry. In: Munnik T, Heilmann I (eds) Plant lipid signaling protocols, Methods in molecular biology (methods and protocols), vol 1009. Humana, Totowa, pp 79–91
Cajka T, Fiehn O (2014) Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry. Trends Analyt Chem 61:192–206
Almeida R, Pauling JK, Sokol E et al (2015) Comprehensive lipidome analysis by shotgun lipidomics on a hybrid quadrupole-orbitrap-linear ion trap mass spectrometer. J Am Soc Mass Spectrom 26:133–148
Annesley TM (2003) Ion suppression in mass spectrometry. Clin Chem 49:1041–1044
Fauland A, Kofeler H, Trotzmuller M et al (2011) A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry. J Lipid Res 52:2314–2322
Okazaki Y, Kamide Y, Hirai MY, Saito K (2013) Plant lipidomics based on hydrophilic interaction chromatography coupled to ion trap time-of-flight mass spectrometry. Metabolomics 9:121–131
Cifkova E, Holcapek M, Lisa M et al (2012) Nontargeted quantitation of lipid classes using hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry with single internal standard and response factor approach. Anal Chem 84:10064–10070
Degenkolbe T, Giavalisco P, Zuther E et al (2012) Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana. Plant J 72:972–982
Salem MA, Juppner J, Bajdzienko K, Giavalisco P (2016) Protocol: a fast, comprehensive and reproducible one-step extraction method for the rapid preparation of polar and semi-polar metabolites, lipids, proteins, starch and cell wall polymers from a single sample. Plant Methods 12:45
Salem M, Bernach M, Bajdzienko K, Giavalisco P (2017) A simple fractionated extraction method for the comprehensive analysis of metabolites, lipids, and proteins from a single sample. J Vis Exp 124:e55802
Lommen A (2009) MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 81:3079–3086
Katajamaa M, Miettinen J, Oresic M (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22:634–636
Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G (2012) XCMS online: a web-based platform to process untargeted metabolomic data. Anal Chem 84:5035–5039
Gowda H, Ivanisevic J, Johnson CH et al (2014) Interactive XCMS online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem 86:6931–6939
Devaiah SP, Roth MR, Baughman E et al (2006) Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a phospholipase Dalpha1 knockout mutant. Phytochemistry 67:1907–1924
Tarazona P, Feussner K, Feussner I (2015) An enhanced plant lipidomics method based on multiplexed liquid chromatography-mass spectrometry reveals additional insights into cold- and drought-induced membrane remodeling. Plant J 84:621–633
Vu HS, Shiva S, Roth MR et al (2014) Lipid changes after leaf wounding in Arabidopsis thaliana: expanded lipidomic data form the basis for lipid co-occurrence analysis. Plant J 80:728–743
Castro-Perez J, Roddy TP, Nibbering NM et al (2011) Localization of fatty acyl and double bond positions in phosphatidylcholines using a dual stage CID fragmentation coupled with ion mobility mass spectrometry. J Am Soc Mass Spectrom 22:1552–1567
Hsu FF, Turk J (2008) Elucidation of the double-bond position of long-chain unsaturated fatty acids by multiple-stage linear ion-trap mass spectrometry with electrospray ionization. J Am Soc Mass Spectrom 19:1673–1680
Poad BL, Pham HT, Thomas MC et al (2010) Ozone-induced dissociation on a modified tandem linear ion-trap: observations of different reactivity for isomeric lipids. J Am Soc Mass Spectrom 21:1989–1999
Acknowledgments
We would like to thank Andrea Leisse and Dr. Vinzenz Hofferek for technical assistance. The Max Planck Society and the DAAD are kindly acknowledged for the generous funding.
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Salem, M.A., Giavalisco, P. (2018). Semi-targeted Lipidomics of Plant Acyl Lipids Using UPLC-HR-MS in Combination with a Data-Independent Acquisition Mode. In: António, C. (eds) Plant Metabolomics. Methods in Molecular Biology, vol 1778. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7819-9_10
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DOI: https://doi.org/10.1007/978-1-4939-7819-9_10
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