A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source

Metabolomics

Volumn 13, Issue 3, 2017, Pages

  Breitkopf, Susanne B ^a,b   Ricoult, Stéphane J H ^c   Yuan, Min ^a   Xu, Ying ^a   Peake, David A ^d   Manning, Brendan D ^c   Asara, John M ^a,b  

^a BETH ISRAEL DEACONESS MEDICAL CENTER   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^d Thermo Fisher Scientific   (United States)

Author keywords

Biomarkers; Cancer; Disease; LC MS MS; Lipidomics; Mass spectrometry; Polarity switching; Profiling; Quantification; Shotgun

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; FATTY ACID; MAMMALIAN TARGET OF RAPAMYCIN COMPLEX 1; PHOSPHATIDYLINOSITOL KINASE; PHOSPHOLIPID; RAPAMYCIN; SPHINGOMYELIN; TERT BUTYL METHYL ETHER; TRIACYLGLYCEROL;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; BREAST TUMOR; CHROMATOGRAPHY; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; DATA ANALYSIS; FEMALE; FIBROBLAST; LIPIDOMICS; LIPOGENESIS; LIQUID CHROMATOGRAPHY; MALIGNANT NEOPLASM; MASS SPECTROMETRY; MOUSE; NONHUMAN; QUANTITATIVE STUDY; REVERSED PHASE LIQUID CHROMATOGRAPHY; SOFT TISSUE;

EID: 85011811012     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-016-1157-8     Document Type: Article

References (66)

1. AHMED, Z., MAYR, M., ZEESHAN, S., DANDEKAR, T., MUELLER, M. J., & FEKETE, A. (2015). Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics (Oxford, England), 31, 1150–1153.
2. Asara, J. M., Xu, Y., Breitkopf, S. B., Yuan, M., Ricoult, S. J. & Manning, B. D. (2016). Preparing Biological Samples for Metabolomics and Lipidomics, Can We Start with Just One Sample? Association of Biomolecular Resource Facilities. Ft. Lauderdale.
3. Ben-Sahra, I., Howell, J. J., Asara, J. M., & Manning, B. D. (2013). Stimulation of de novo pyrimidine synthesis by growth signaling through mTOR and S6K1. Science, 339, 1323–1328.
4. Bilgin, M., Born, P., Fezza, F., Heimes, M., Mastrangelo, N., Wagner, N., Schultz, C., Maccarrone, M., Eaton, S., Nadler, A., Wilm, M., & Shevchenko, A. (2016). Lipid Discovery by Combinatorial Screening and Untargeted LC-MS/MS. Scientific Reports, 6, 27920.
5. Bird, S. S., Marur, V. R., Sniatynski, M. J., Greenberg, H. K., & Kristal, B. S. (2011). Serum lipidomics profiling using LC-MS and high-energy collisional dissociation fragmentation: focus on triglyceride detection and characterization. Analytical Chemistry, 83, 6648–6657.
6. Breitkopf, S. B., Yuan, M., Helenius, K. P., Lyssiotis, C. A., & Asara, J. M. (2015). Triomics analysis of imatinib-treated myeloma cells connects kinase inhibition to RNA processing and decreased lipid biosynthesis. Analytical Chemistry, 87(21), 10995–11006
7. Breitkopf, S. B., Yuan, M., XU, Y., & Asara, J. M. 2016. A quantitative positive/negative ion switching method for shotgun lipidomics via high resolution LC-MS/MS from any biological source. San Antonio: American Society for Mass Spectrometry
8. Cajka, T., & Fiehn, O. (2014). Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry. Trends In Analytical Chemistry, 61, 192–206.
9. Chou, C. H., Chang, W. C., Chiu, C. M., Huang, C. C., & Huang, H. D. (2009). FMM: A web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Research, 37, W129–W134.
10. Collins, J. R., Edwards, B. R., Fredricks, H. F., & van MOOY, B. A. (2016). LOBSTAHS: An adduct-based lipidomics strategy for discovery and identification of oxidative stress biomarkers. Analytical Chemistry, 88, 7154–7162.
11. COOMBS, K. M. (2011). Quantitative proteomics of complex mixtures. Expert Review of Proteomics, 8, 659–677.
12. COX, J., & MANN, M (2011). Quantitative, high-resolution proteomics for data-driven systems biology. Annual Review of Biochemistry, 80, 273–299.
13. Duvel, K., Yecies, J. L., Menon, S., Raman, P., Lipovsky, A. I., Souza, A. L., Triantafellow, E., Ma, Q., Gorski, R., Cleaver, S., Vander Heiden, M. G., Mackeigan, J. P., Finan, P. M., Clish, C. B., Murphy, L. O., & Manning, B. D. (2010). Activation of a metabolic gene regulatory network downstream of mTOR complex 1. Molecular Cell, 39, 171–183.
14. Fahy, E., Sud, M., Cotter, D., & Subramaniam, S. (2007). LIPID MAPS online tools for lipid research. Nucleic Acids Research, 35, W606–W612.
15. Fauland, A., Kofeler, H., Trotzmuller, M., Knopf, A., Hartler, J., Eberl, A., Chitraju, C., Lankmayr, E., & Spener, F. (2011). A comprehensive method for lipid profiling by liquid chromatography-ion cyclotron resonance mass spectrometry. Journal of Lipid Research, 52, 2314–2322.
16. Folch, J., Lees, M., & Sloane Stanley, G. H. (1957). A simple method for the isolation and purification of total lipides from animal tissues. The Journal of Biological Chemistry, 226, 497–509.
17. Godzien, J., Ciborowski, M., Martinez-Alcazar, M. P., Samczuk, P., Kretowski, A., & Barbas, C. (2015). Rapid and reliable identification of phospholipids for untargeted metabolomics with LC-ESI-QTOF-MS/MS. Journal of Proteome Research, 14, 3204–3216.
18. Han, X., Yang, K., & Gross, R. W. (2012). Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses. Mass Spectrometry Reviews, 31, 134–178.
19. Hara, H., Uchimura, T., Akashi, N., Naganuma, T., Aizawa, T., Nagae, Y., & Masuda, N. (2004). Simultaneous analytical method for the determination of TCH346 and its four metabolites in human plasma by liquid chromatography/tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 18, 377–384.
20. Hartler, J., Trotzmuller, M., Chitraju, C., Spener, F., Kofeler, H. C., & Thallinger, G. G. (2011). Lipid data analyzer: Unattended identification and quantitation of lipids in LC-MS data. Bioinformatics (Oxford, England), 27, 572–577.
21. Hein, E. M., Bodeker, B., Nolte, J., & Hayen, H. (2010). Software tool for mining liquid chromatography/multi-stage mass spectrometry data for comprehensive glycerophospholipid profiling. Rapid Communications in Mass Spectrometry, 24, 2083–2092.
22. Hopperton, K. E., Duncan, R. E., Bazinet, R. P., & Archer, M. C. (2014). Fatty acid synthase plays a role in cancer metabolism beyond providing fatty acids for phospholipid synthesis or sustaining elevations in glycolytic activity. Experimental Cell Research, 320, 302–310.
23. Horton, J. D., Goldstein, J. L., & Brown, M. S. (2002). SREBPs: Activators of the complete program of cholesterol and fatty acid synthesis in the liver. The Journal of Clinical Investigation, 109, 1125–1131.
24. Hou, W., Zhou, H., Bou Khalil, M., Seebun, D., Bennett, S. A., & Figeys, D. (2011). Lyso-form fragment ions facilitate the determination of stereospecificity of diacyl glycerophospholipids. Rapid Communications in Mass Spectrometry, 25, 205–217.
25. Houjou, T., Yamatani, K., Imagawa, M., Shimizu, T., & Taguchi, R. (2005). A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry. Rapid Communications in Mass Spectrometry, 19, 654–666.
26. Junot, C., Fenaille, F., Colsch, B., & Becher, F. (2014). High resolution mass spectrometry based techniques at the crossroads of metabolic pathways. Mass Spectrometry Reviews, 33, 471–500.
27. Kasiske, B. L., De Mattos, A., Flechner, S. M., Gallon, L., Meier-Kriesche, H. U., Weir, M. R., & Wilkinson, A. (2008). Mammalian target of rapamycin inhibitor dyslipidemia in kidney transplant recipients. American Journal of Transplantation, 8, 1384–1392.
28. Kluger, B., Bueschl, C., Neumann, N., Stuckler, R., Doppler, M., Chassy, A. W., Waterhouse, A. L., Rechthaler, J., Kampleitner, N., Thallinger, G. G., Adam, G., Krska, R., & Schuhmacher, R. (2014). Untargeted profiling of tracer-derived metabolites using stable isotopic labeling and fast polarity-switching LC-ESI-HRMS. Analytical Chemistry, 86, 11533–11537.
29. Kofeler, H. C., FAULAND, A., RECHBERGER, G. N., & TROTZMULLER, M. (2012). Mass spectrometry based lipidomics: an overview of technological platforms. Metabolites, 2, 19–38.
30. Koyama, J., Taga, S., Shimizu, K., Shimizu, M., Morita, I., & Takeuchi, A. (2011). Simultaneous determination of histamine and prostaglandin D2 using an LC–ESI–MS/MS method with positive/negative ion-switching ionization modes: Application to the study of anti-allergic flavonoids on the degranulation of KU812 cells. Analytical and Bioanalytical Chemistry, 401, 1385–1392.
31. Kwiatkowski, D. J., & Manning, B. D. (2014). Molecular basis of giant cells in tuberous sclerosis complex. The New England Journal of Medicine, 371, 778–780.
32. Lam, S. M., & Shui, G (2013). Lipidomics as a principal tool for advancing biomedical research. Journal of Genetics and Genomics, 40, 375–390.
33. Li, M., Yang, L., Bai, Y., & Liu, H. (2014). Analytical methods in lipidomics and their applications. Analytical Chemistry, 86, 161–175.
34. Linden, M. A., Lopez, K. T., Fletcher, J. A., Morris, E. M., Meers, G. M., Siddique, S., Laughlin, M. H., Sowers, J. R., Thyfault, J. P., Ibdah, J. A., & Rector, R. S. (2015). Combining metformin therapy with caloric restriction for the management of type 2 diabetes and nonalcoholic fatty liver disease in obese rats. Applied Physiology, Nutrition, and Metabolism, 40, 1038–1047.
35. Ma, S., & Chowdhury, S. K. (2013). Data acquisition and data mining techniques for metabolite identification using LC coupled to high-resolution MS. Bioanalysis, 5, 1285–1297.
36. Matyash, V., Liebisch, G., Kurzchalia, T. V., Shevchenko, A., & Schwudke, D. (2008). Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. Journal of Lipid Research, 49, 1137–1146.
37. Menendez, J. A., & Lupu, R (2007). Fatty acid synthase and the lipogenic phenotype in cancer pathogenesis. Nature Reviews, 7, 763–777.
38. Min, H. K., Lim, S., Chung, B. C., & Moon, M. H. (2011). Shotgun lipidomics for candidate biomarkers of urinary phospholipids in prostate cancer. Analytical and Bioanalytical Chemistry, 399, 823–830.
39. Morrisett, J. D., Abdel-Fattah, G., Hoogeveen, R., Mitchell, E., Ballantyne, C. M., Pownall, H. J., Opekun, A. R., Jaffe, J. S., Oppermann, S., & Kahan, B. D. (2002). Effects of sirolimus on plasma lipids, lipoprotein levels, and fatty acid metabolism in renal transplant patients. Journal of Lipid Research, 43, 1170–1180.
40. Narvaez-Rivas, M., & Zhang, Q (2016). Comprehensive untargeted lipidomic analysis using core–shell C30 particle column and high field orbitrap mass spectrometer. Journal of Chromatography A, 1440, 123–134.
41. Nicolay, B. N., Gameiro, P. A., Tschop, K., Korenjak, M., Heilmann, A. M., Asara, J. M., Stephanopoulos, G., Iliopoulos, O., & Dyson, N. J. (2013). Loss of RBF1 changes glutamine catabolism. Genes and Development, 27, 182–196.
42. Peake, D. A., Yokoi, Y., Wang, J. & Huang, Y. (2013). A New Lipid Software Workflow for Processing Orbitrap-based Global Lipidomics Data in Translational and Systems Biology Research. http://www.thermoscientific.com.
43. Porstmann, T., Santos, C. R., Griffiths, B., Cully, M., Wu, M., Leevers, S., Griffiths, J. R., Chung, Y. L., & Schulze, A. (2008). SREBP activity is regulated by mTORC1 and contributes to Akt-dependent cell growth. Cell Metabolism, 8, 224–236.
44. Ricoult, S. J., & Manning, B. D. (2013). The multifaceted role of mTORC1 in the control of lipid metabolism. EMBO Reports, 14, 242–251.
45. Ricoult, S. J., Yecies, J. L., Ben-Sahra, I., & Manning, B. D. (2015). Oncogenic PI3K and K-Ras stimulate de novo lipid synthesis through mTORC1 and SREBP. Oncogene, 35(10), 1250–1260
46. Rodamer, M., Elsinghorst, P. W., Kinzig, M., Gutschow, M., & Sorgel, F. (2011). Development and validation of a liquid chromatography/tandem mass spectrometry procedure for the quantification of sunitinib (SU11248) and its active metabolite, N-desethyl sunitinib (SU12662), in human plasma: Application to an explorative study. Journal of Chromatography B, 879, 695–706.
47. Rolim, A. E., Henrique-Araujo, R., Ferraz, E. G., Dultra, F. K. D. A. A., & Fernandez, L. G. (2015). Lipidomics in the study of lipid metabolism: Current perspectives in the omic sciences. Gene, 554, 131–139.
48. Sajic, T., Liu, Y., & Aebersold, R. (2015). Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clinical Applications, 9, 307–321.
49. Schwudke, D., Schuhmann, K., Herzog, R., Bornstein, S. R., & Shevchenko, A. (2011). Shotgun lipidomics on high resolution mass spectrometers. Cold Spring Harbor Perspectives in Biology, 3, a004614.
50. Tate, S., Larsen, B., Bonner, R., & Gingras, A. C. (2013). Label-free quantitative proteomics trends for protein–protein interactions. Journal of Proteomics, 81, 91–101.
51. Theodoridis, G. A., Gika, H. G., Want, E. J., & Wilson, I. D. (2012). Liquid chromatography-mass spectrometry based global metabolite profiling: A review. Analytica Chimica Acta, 711, 7–16.
52. Tyurina, Y. Y., Domingues, R. M., Tyurin, V. A., Maciel, E., Domingues, P., Amoscato, A. A., Bayir, H., & Kagan, V. E. (2014). Characterization of cardiolipins and their oxidation products by LC-MS analysis. Chemistry and Physics of Lipids, 179, 3–10.
53. van der Kloet, F. M., Hendriks, M., Hankemeier, T., & Reijmers, T. (2013). A new approach to untargeted integration of high resolution liquid chromatography-mass spectrometry data. Analytica Chimica Acta, 801, 34–42.
54. Vaz, F. M., Pras-Raves, M., Bootsma, A. H., & van Kampen, A. H. (2015). Principles and practice of lipidomics. Journal of Inherited Metabolic Disease, 38, 41–52.
55. Wang, C., Wang, M., & HAN, X. (2015). Applications of mass spectrometry for cellular lipid analysis. Molecular Biosystems, 11, 698–713.
56. Wishart, D. S., Knox, C., Guo, A. C., Eisner, R., Young, N., Gautam, B., Hau, D. D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., XIA, J., Jia, L., Cruz, J. A., Lim, E., Sobsey, C. A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., de Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., LI, L., VOGEL, H. J., & FORSYTHE, I. (2009). HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research, 37, D603–D610.
57. Xia, J., Psychogios, N., Young, N., & Wishart, D. S. (2009). MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Research, 37, W652–W660.
58. Xia, J., & Wishart, D. S. (2011). Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst. Nature Protocols, 6, 743–760.
59. Xiao, J. F., Zhou, B., & Ressom, H. W. (2012). Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends in Analytical Chemistry, 32, 1–14.
60. Yamada, T., Uchikata, T., Sakamoto, S., Yokoi, Y., Fukusaki, E., & Bamba, T. (2013a). Development of a lipid profiling system using reverse-phase liquid chromatography coupled to high-resolution mass spectrometry with rapid polarity switching and an automated lipid identification software. Journal of Chromatography A, 1292, 211–218.
61. Yamada, T., Uchikata, T., Sakamoto, S., Yokoi, Y., Nishiumi, S., Yoshida, M., Fukusaki, E., & Bamba, T. (2013b). Supercritical fluid chromatography/Orbitrap mass spectrometry based lipidomics platform coupled with automated lipid identification software for accurate lipid profiling. Journal of Chromatography A, 1301, 237–242.
62. Yang, K., Jenkins, C. M., Dilthey, B., & Gross, R. W. (2015). Multidimensional mass spectrometry-based shotgun lipidomics analysis of vinyl ether diglycerides. Analytical and Bioanalytical Chemistry, 407, 5199–5210.
63. Yecies, J. L., Zhang, H. H., Menon, S., Liu, S., Yecies, D., Lipovsky, A. I., Gorgun, C., Kwiatkowski, D. J., Hotamisligil, G. S., Lee, C. H., & Manning, B. D. (2011). Akt stimulates hepatic SREBP1c and lipogenesis through parallel mTORC1-dependent and independent pathways. Cell Metabolism, 14, 21–32.
64. Ying, H., Kimmelman, A. C., Lyssiotis, C. A., Hua, S., Chu, G. C., Fletcher-Sananikone, E., Locasale, J. W., Son, J., Zhang, H., Coloff, J. L., Yan, H., Wang, W., Chen, S., Viale, A., Zheng, H., PAIK, J. H., LIM, C., Guimaraes, A. R., Martin, E. S., Chang, J., Hezel, A. F., Perry, S. R., Hu, J., Gan, B., Xiao, Y., Asara, J. M., Weissleder, R., Wang, Y. A., Chin, L., Cantley, L. C., & Depinho, R. A. (2012). Oncogenic Kras maintains pancreatic tumors through regulation of anabolic glucose metabolism. Cell, 149, 656–670.
65. Yuan, M., Breitkopf, S. B., Yang, X., & Asara, J. M. (2012). A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nature Protocols, 7, 872–881.
66. Zhang, Y., Ren, Y., Jiao, J., & Li, D. (2011). Ultra high-performance liquid chromatography-tandem mass spectrometry for the simultaneous analysis of asparagine, sugars, and acrylamide in Maillard reactions. Anal Chem, 83, 3297–3304.