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Lipidomics: Mass Spectrometry Based Untargeted Profiling and False Positives

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Lipidomics in Health & Disease

Part of the book series: Translational Bioinformatics ((TRBIO,volume 14))

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Abstract

Lipid metabolism is increasingly popular in recent years. Lipidomics analysis is the most powerful technique for large scale analysis of lipid molecules. Untargeted lipidomics using high resolution mass spectrometry is the mainstream due to the wide coverage of lipids. This review discusses the major platforms of untargeted lipidomics from lipid extraction to molecular assignment. Various false positives are also summarized to improve the confidence of untargeted lipidomic analysis. Quantitation of cellular or organellar lipid composition is essential to understand lipid physiological function. Therefore, the approaches of quantifying different lipids are included in this review.

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References

  • Abbassighadi N, Jones EA, Gomezromero M, et al. A comparison of DESI-MS and LC-MS for the lipidomic profiling of human cancer tissue[J]. J Am Soc Mass Spectrom. 2016;27:255–64.

    Article  CAS  Google Scholar 

  • Bamba T, Lee JW, Matsubara A, Fukusaki E. Metabolic profiling of lipids by supercritical fluid chromatography/mass spectrometry. J Chromatogr A. 2012;1250:212–9.

    Article  CAS  PubMed  Google Scholar 

  • Bird SS, Marur VR, Sniatynski MJ, Greenberg HK, Kristal BS. Serum lipidomics profiling using LC-MS and high-energy collisional dissociation fragmentation: focus on triglyceride detection and characterization. Anal Chem. 2011a;83:6648–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bird SS, Marur VR, Sniatynski MJ, Greenberg HK, Kristal BS. Lipidomics profiling by high-resolution LC-MS and high-energy collisional dissociation fragmentation: focus on characterization of mitochondrial cardiolipins and monolysocardiolipins. Anal Chem. 2011b;83:940–9.

    Article  CAS  PubMed  Google Scholar 

  • Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Biochem Cell Biol. 1959;37:911–7.

    CAS  Google Scholar 

  • Bou Khalil M, Hou W, Zhou H, Elisma F, Swayne LA, Blanchard AP, Yao Z, Bennett SA, Figeys D. Lipidomics era: accomplishments and challenges. Mass Spectrom Rev. 2010;29:877–929.

    Article  CAS  PubMed  Google Scholar 

  • Breitkopf SB, Ricoult SJH, Yuan M, Xu Y, Peake DA, Manning BD, Asara JM. A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source. Metab: Official J Metab Soc. 2017;13(3):30.

    Google Scholar 

  • Brugger B. Lipidomics: analysis of the lipid composition of cells and subcellular organelles by electrospray ionization mass spectrometry. Annu Rev Biochem. 2014;83:79–98.

    Article  CAS  PubMed  Google Scholar 

  • Cajka T, Fiehn O. Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry. Trends Analyt Chem: TRAC. 2014;61:192–206.

    Article  CAS  PubMed  Google Scholar 

  • Cajka T, Fiehn O. Toward merging untargeted and targeted methods in mass spectrometry-based metabolomics and lipidomics. Anal Chem. 2016;88:524–45.

    Article  CAS  PubMed  Google Scholar 

  • Cequier-Sánchez E, Rodríguez C, Ravelo ÁG, Zárate R. Dichloromethane as a solvent for lipid extraction and assessment of lipid classes and fatty acids from samples of different natures. J Agric Food Chem. 2008;56:4297–303.

    Article  CAS  PubMed  Google Scholar 

  • Chen S, Hoene M, Li J, Li Y, Zhao X, Haring HU, Schleicher ED, Weigert C, Xu G, Lehmann R. Simultaneous extraction of metabolome and lipidome with methyl tert-butyl ether from a single small tissue sample for ultra-high performance liquid chromatography/mass spectrometry. J Chromatogr A. 2013;1298:9–16.

    Article  CAS  PubMed  Google Scholar 

  • Clark J, Anderson KE, Juvin V, Smith TS, Karpe F, Wakelam MJ, Stephens LR, Hawkins PT. Quantification of PtdInsP3 molecular species in cells and tissues by mass spectrometry. Nat Methods. 2011;8:267–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clendinen CS, Monge ME, Fernandez FM. Ambient mass spectrometry in metabolomics. Analyst. 2017;142:3101–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eberlin LS, Liu X, Ferreira CR, Santagata S, Agar NY, Cooks RG. Desorption electrospray ionization then MALDI mass spectrometry imaging of lipid and protein distributions in single tissue sections. Anal Chem. 2011;83:8366–71.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fenaille F, Barbier Saint-Hilaire P, Rousseau K, Junot C. Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: where do we stand? J Chromatogr A. 2017;1526:1–12.

    Article  CAS  PubMed  Google Scholar 

  • Folch J, Lees M, Sloane Stanley GH. A simple method for the isolation and purification of totallipides from animal tissues. J Biol Chem. 1957;226:497–509.

    PubMed  CAS  Google Scholar 

  • Granafei S, Azzone P, Spinelli VA, Losito I, Palmisano F, Cataldi TRI. Hydrophilic interaction and reversed phase mixed-mode liquid chromatography coupled to high resolution tandem mass spectrometry for polar lipids analysis. J Chromatogr A. 2016;1477:47–55.

    Article  CAS  PubMed  Google Scholar 

  • Gregory KE, Bird SS, Gross VS, Marur VR, Lazarev AV, Walker WA, Kristal BS. Method development for fecal lipidomics profiling. Anal Chem. 2013;85:1114–23.

    Article  CAS  PubMed  Google Scholar 

  • Gross RW. The evolution of lipidomics through space and time. Biochim Biophys Acta. 2017;1862:731–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han X, Yang K, Gross RW. Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses. Mass Spectrom Rev. 2012;31:134–78.

    Article  CAS  PubMed  Google Scholar 

  • Han J, Liu Y, Wang R, Yang J, Ling V, Borchers CH. Metabolic profiling of bile acids in human and mouse blood by LC-MS/MS in combination with phospholipid-depletion solid-phase extraction. Anal Chem. 2015;87:1127–36.

    Article  CAS  PubMed  Google Scholar 

  • Hu C, Wang M, Han X. Shotgun lipidomics in substantiating lipid peroxidation in redox biology: methods and applications. Redox Biol. 2017;12:946–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kind T, Liu KH, Lee DY, DeFelice B, Meissen JK, Fiehn O. LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat Methods. 2013;10:755–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laboureur L, Ollero M, Touboul D. Lipidomics by supercritical fluid chromatography. Int J Mol Sci. 2015;16:13868–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lam SM, Shui G. Lipidomics as a principal tool for advancing biomedical research. J Genet Genomics Yi chuan xue bao. 2013;40:375–90.

    Article  CAS  PubMed  Google Scholar 

  • Lam SM, Tong L, Duan X, Petznick A, Wenk MR, Shui G. Extensive characterization of human tear fluid collected using different techniques unravels the presence of novel lipid amphiphiles. J Lipid Res. 2014;55:289–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lam SM, Tian H, Shui G. Lipidomics, en route to accurate quantitation. Biochim Biophys Acta. 2017;1862:752–61.

    Article  CAS  PubMed  Google Scholar 

  • Li M, Feng B, Liang Y, Zhang W, Bai Y, Tang W, Wang T, Liu H. Lipid profiling of human plasma from peritoneal dialysis patients using an improved 2D (NP/RP) LC-QToF MS method. Anal Bioanal Chem. 2013;405:6629–38.

    Article  CAS  PubMed  Google Scholar 

  • Li M, Yang L, Bai Y, Liu H. Analytical methods in lipidomics and their applications. Anal Chem. 2014a;86:161–75.

    Article  CAS  PubMed  Google Scholar 

  • Li M, Tong X, Lv P, Feng B, Yang L, Wu Z, Cui X, Bai Y, Huang Y, Liu H. A not-stop-flow online normal−/reversed-phase two-dimensional liquid chromatography-quadrupole time-of-flight mass spectrometry method for comprehensive lipid profiling of human plasma from atherosclerosis patients. J Chromatogr A. 2014b;1372C:110–9.

    Article  CAS  PubMed  Google Scholar 

  • Li H, Cai Y, Guo Y, Chen F, Zhu ZJ. MetDIA: targeted metabolite extraction of multiplexed MS/MS spectra generated by data-independent acquisition. Anal Chem. 2016;88:8757–64.

    Article  CAS  PubMed  Google Scholar 

  • Lisa M, Holcapek M. High-throughput and comprehensive Lipidomic analysis using ultrahigh-performance supercritical fluid chromatography-mass spectrometry. Anal Chem. 2015;87:7187–95.

    Article  CAS  PubMed  Google Scholar 

  • Lisa M, Cifkova E, Khalikova M, Ovcacikova M, Holcapek M. Lipidomic analysis of biological samples: comparison of liquid chromatography, supercritical fluid chromatography and direct infusion mass spectrometry methods. J Chromatogr A. 2017;1525:96–108.

    Article  CAS  PubMed  Google Scholar 

  • Meikle PJ, Wong G, Barlow CK, Kingwell BA. Lipidomics: potential role in risk prediction and therapeutic monitoring for diabetes and cardiovascular disease. Pharmacol Ther. 2014;143:12–23.

    Article  CAS  PubMed  Google Scholar 

  • Murphy RC, Axelsen PH. Mass spectrometric analysis of long-chain lipids. Mass Spectrom Rev. 2011;30:579–99.

    Article  CAS  PubMed  Google Scholar 

  • Narvaez-Rivas M, Zhang Q. Comprehensive untargeted lipidomic analysis using core-shell C30 particle column and high field orbitrap mass spectrometer. J Chromatogr A. 2016;1440:123–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patterson RE, Ducrocq AJ, McDougall DJ, Garrett TJ, Yost RA. Comparison of blood plasma sample preparation methods for combined LC-MS lipidomics and metabolomics. J Chromatog B Analyt Technol Biomed Life Sci. 2015;1002:260–6.

    Article  CAS  Google Scholar 

  • Pellegrino RM, Di Veroli A, Valeri A, Goracci L, Cruciani G. LC/MS lipid profiling from human serum: a new method for global lipid extraction. Anal Bioanal Chem. 2014;406:7937–48.

    Article  CAS  PubMed  Google Scholar 

  • Prasain JK, Wilson L, Hoang HD, Moore R, Miller MA. Comparative lipidomics of Caenorhabditis elegans metabolic disease models by SWATH non-targeted tandem mass spectrometry. Meta. 2015;5:677–96.

    CAS  Google Scholar 

  • Reis A, Rudnitskaya A, Blackburn GJ, Mohd Fauzi N, Pitt AR, Spickett CM. A comparison of five lipid extraction solvent systems for lipidomic studies of human LDL. J Lipid Res. 2013;54:1812–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rocha B, Cillero-Pastor B, Blanco FJ, Ruiz-Romero C. MALDI mass spectrometry imaging in rheumatic diseases. Biochim Biophys Acta. 2017;1865:784–94.

    Article  CAS  Google Scholar 

  • Sarafian MH, Gaudin M, Lewis MR, Martin FP, Holmes E, Nicholson JK, Dumas ME. Objective set of criteria for optimization of sample preparation procedures for ultra-high throughput untargeted blood plasma lipid profiling by ultra performance liquid chromatography-mass spectrometry. Anal Chem. 2014;86:5766–74.

    Article  CAS  PubMed  Google Scholar 

  • Satomi Y, Hirayama M, Kobayashi H. One-step lipid extraction for plasma lipidomics analysis by liquid chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1063:93–100.

    Article  CAS  PubMed  Google Scholar 

  • Schuhmann K, Almeida R, Baumert M, Herzog R, Bornstein SR, Shevchenko A. Shotgun lipidomics on a LTQ Orbitrap mass spectrometer by successive switching between acquisition polarity modes. J Mass Spectrom: JMS. 2012;47:96–104.

    Article  CAS  PubMed  Google Scholar 

  • Shen Q, Dai Z, Huang YW, Cheung HY. Lipidomic profiling of dried seahorses by hydrophilic interaction chromatography coupled to mass spectrometry. Food Chem. 2016;205:89–96.

    Article  CAS  PubMed  Google Scholar 

  • Stephenson DJ, Hoeferlin LA, Chalfant CE. Lipidomics in translational research and the clinical significance of lipid-based biomarkers. Transl Res: The J Lab Clin Med. 2017;189:13–29.

    Article  CAS  Google Scholar 

  • Strassburg K, Huijbrechts AM, Kortekaas KA, Lindeman JH, Pedersen TL, Dane A, Berger R, Brenkman A, Hankemeier T, van Duynhoven J, Kalkhoven E, Newman JW, Vreeken RJ. Quantitative profiling of oxylipins through comprehensive LC-MS/MS analysis: application in cardiac surgery. Anal Bioanal Chem. 2012;404:1413–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang H, Wang X, Xu L, Ran X, Li X, Chen L, Zhao X, Deng H, Liu X. Establishment of local searching methods for orbitrap-based high throughput metabolomics analysis. Talanta. 2016;156-157:163–71.

    Article  CAS  PubMed  Google Scholar 

  • Tipthara P, Thongboonkerd V. Differential human urinary lipid profiles using various lipid-extraction protocols: MALDI-TOF and LIFT-TOF/TOF analyses. Sci Rep. 2016;6:33756.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tipthara P, Kunacheva C, Soh YN, Wong SC, Pin NS, Stuckey DC, Boehm BO. Global profiling of metabolite and lipid soluble microbial products in anaerobic wastewater reactor supernatant using UPLC-MS(E). J Proteome Res. 2017;16:559–70.

    Article  CAS  PubMed  Google Scholar 

  • Triebl A, Trotzmuller M, Eberl A, Hanel P, Hartler J, Kofeler HC. Quantitation of phosphatidic acid and lysophosphatidic acid molecular species using hydrophilic interaction liquid chromatography coupled to electrospray ionization high resolution mass spectrometry. J Chromatogr A. 2014;1347:104–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods. 2015;12:523–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tu J, Yin Y, Xu M, Wang R, Zhu Z-J. Absolute quantitative lipidomics reveals lipidome-wide alterations in aging brain. Metab: Off J Metab Soc. 2017;14:1–11.

    Google Scholar 

  • Ucal Y, Durer ZA, Atak H, Kadioglu E, Sahin B, Coskun A, Baykal AT, Ozpinar A. Clinical applications of MALDI imaging technologies in cancer and neurodegenerative diseases. Biochim Biophys Acta. 2017;1865:795–816.

    Article  CAS  Google Scholar 

  • Wang M, Huang Y, Han X. Accurate mass searching of individual lipid species candidates from high-resolution mass spectra for shotgun lipidomics. Rapid Commun Mass Spectrom: RCM. 2014;28:2201–10.

    Article  CAS  PubMed  Google Scholar 

  • Wang M, Palavicini JP, Cseresznye A, Han X. Strategy for quantitative analysis of isomeric Bis(monoacylglycero)phosphate and phosphatidylglycerol species by shotgun Lipidomics after one-step methylation. Anal Chem. 2017a;89:8490–5.

    Article  CAS  PubMed  Google Scholar 

  • Wang M, Wang C, Han X. Selection of internal standards for accurate quantification of complex lipid species in biological extracts by electrospray ionization mass spectrometry-what, how and why? Mass Spectrom Rev. 2017b;36:693–714.

    Article  CAS  PubMed  Google Scholar 

  • Want EJ, Masson P, Michopoulos F, Wilson ID, Theodoridis G, Plumb RS, Shockcor J, Loftus N, Holmes E, Nicholson JK. Global metabolic profiling of animal and human tissues via UPLC-MS. Nat Protoc. 2013;8:17–32.

    Article  CAS  PubMed  Google Scholar 

  • Wenk MR. Lipidomics: new tools and applications. Cell. 2010;143:888–95.

    Article  CAS  PubMed  Google Scholar 

  • Xu YF, Lu W, Rabinowitz JD. Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics. Anal Chem. 2015;87:2273–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu L, Wang X, Jiao Y, Liu X. Assessment of potential false positives via orbitrap-based untargeted lipidomics from rat tissues. Talanta. 2018;178:287–93.

    Article  CAS  PubMed  Google Scholar 

  • Yang K, Han X. Lipidomics: techniques, applications, and outcomes related to biomedical sciences. Trends Biochem Sci. 2016;41:954–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yuan M, Breitkopf SB, Yang X, Asara JM. A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc. 2012;7:872–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J, Yu W, Suliburk J, Eberlin LS. Will ambient ionization mass spectrometry become an integral Technology in the operating room of the future? Clin Chem. 2016;62:1172–4.

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Gao Y, Sun J, Fan S, Yao X, Ran X, Zheng C, Huang M, Bi H. Optimization of lipid extraction and analytical protocols for UHPLC-ESI-HRMS-based lipidomic analysis of adherent mammalian cancer cells. Anal Bioanal Chem. 2017;409:5349–58.

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Li Y, Chen X, Zhong L, Yin Y. Development of data-independent acquisition workflows for metabolomic analysis on a quadrupole-orbitrap platform. Talanta. 2017;164:128–36.

    Article  CAS  PubMed  Google Scholar 

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Liu, X., Xu, L., Wang, X., Jiao, Y. (2018). Lipidomics: Mass Spectrometry Based Untargeted Profiling and False Positives. In: Wang, X., Wu, D., Shen, H. (eds) Lipidomics in Health & Disease. Translational Bioinformatics, vol 14. Springer, Singapore. https://doi.org/10.1007/978-981-13-0620-4_10

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