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The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry

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Abstract

Mass spectrometry (MS) has been a major driver for metabolomics, and gas chromatography (GC)-MS has been one of the primary techniques used for microbial metabolomics. The use of liquid chromatography (LC)-MS has however been limited, but electrospray ionization (ESI) is very well suited for ionization of microbial metabolites without any previous derivatization needed. To address the capabilities of ESI-MS in detecting the metabolome of Saccharomyces cerevisiae, the in silico metabolome of this organism was used as a template to present a theoretical metabolome. This showed that in combination with the specificity of MS up to 84% of the metabolites can be identified in a high mass accuracy ESI-spectrum. A total of 66 metabolites were systematically analyzed by positive and negative ESI-MS/MS with the aim of initiating a spectral library for ESI of microbial metabolites. This systematic analysis gave insight into the ionization and fragmentation characteristics of the different metabolites. With this insight, a small study of metabolic footprinting with ESI-MS demonstrated that biological information can be extracted from footprinting spectra. Statistical analysis of the footprinting data revealed discriminating ions, which could be assigned using the in silico metabolome. By this approach metabolic footprinting can advance from a classification method that is used to derive biological information based on guilt-by-association, to a tool for extraction of metabolic differences, which can guide new targeted biological experiments.

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References

  • Allen, J., Davey, H. M., Broadhurst, D., Heald, J. K., Rowland, J. J., Oliver, S. G., et al. (2003). High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nature Biotechnology, 21, 692–696. doi:10.1038/nbt823.

    Article  PubMed  CAS  Google Scholar 

  • Boernsen, K. O., Gatzek, S., & Imbert, G. (2005). Controlled protein precipitation in combination with chip-based nanospray infusion mass spectrometry. An approach for metabolomics profiling of plasma. Analytical Chemistry, 77, 7255–7264. doi:10.1021/ac0508604.

    Article  PubMed  CAS  Google Scholar 

  • Brachmann, C. B., Davies, A., Cost, G. J., Caputo, E., Li, J., Hieter, P., et al. (1998). Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast (Chichester, England), 14, 115–132. doi:10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2.

    Article  CAS  Google Scholar 

  • Bristow, A. W. T., Nichols, W. F., Webb, K. S., & Conway, B. (2002). Evaluation of protocols for reproducible electrospray in-source collisionally induced dissociation on various liquid chromatography/mass spectrometry instruments and the development of spectral libraries. Rapid Communications in Mass Spectrometry, 16, 2374–2386. doi:10.1002/rcm.843.

    Article  PubMed  CAS  Google Scholar 

  • Bristow, A. W. T., Webb, K. S., Lubben, A. T., & Halket, J. (2004). Reproducible product-ion tandem mass spectra on various liquid chromatography/mass spectrometry instruments for the development of spectral libraries. Rapid Communications in Mass Spectrometry, 18, 1447–1454. doi:10.1002/rcm.1492.

    Article  PubMed  CAS  Google Scholar 

  • Castrillo, J. I., Hayes, A., Mohammed, S., Gaskell, S. J., & Oliver, S. G. (2003). An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry, 62, 929–937. doi:10.1016/S0031-9422(02)00713-6.

    Article  PubMed  CAS  Google Scholar 

  • Coulier, L., Bas, R., Jespersen, S., Verheij, E. R., van der Werf, M. J., & Hankemeier, T. (2006). Simultaneous quantitative analysis of metabolites using ion pair-liquid chromatography–electrospray ionization mass spectrometry. Analytical Chemistry, 78, 6573–6582. doi:10.1021/ac0607616.

    Article  PubMed  CAS  Google Scholar 

  • Diderich, J. A., Raamsdonk, L. M., Kruckeberg, A. L., Berden, J. A., & van Dam, K. (2001). Physiological properties of Saccharomyces cerevisiae from which hexokinase II has been deleted. Applied and Environmental Microbiology, 67, 1587–1593. doi:10.1128/AEM.67.4.1587-1593.2001.

    Article  PubMed  CAS  Google Scholar 

  • Dunn, W. B. (2008). Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes. Physical Biology, 5, 1–24. doi:10.1088/1478-3975/5/1/011001.

    Article  Google Scholar 

  • Entian, K.-D., & Mecke, D. (1982). Genetic evidence for a role of hexokinase isozyme PII in carbon catabolite repression in Saccharomyces cerevisiae. The Journal of Biological Chemistry, 257, 870–874.

    PubMed  CAS  Google Scholar 

  • Fiehn, O. (2002). Metabolomics––the link between genotypes and phenotypes. Plant Molecular Biology, 48, 155–171. doi:10.1023/A:1013713905833.

    Article  PubMed  CAS  Google Scholar 

  • Forster, J., Famili, I., Fu, P., Palsson, B. O., & Nielsen, J. (2003). Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Research, 13, 244–253. doi:10.1101/gr.234503.

    Article  PubMed  CAS  Google Scholar 

  • Gergov, M., Weinmann, W., Meriluoto, J., Uusitalo, J., & Ojanpera, I. (2004). Comparison of product ion spectra obtained by liquid chromatography/triple-quadrupole mass spectrometry for library search. Rapid Communications in Mass Spectrometry, 18, 1039–1046. doi:10.1002/rcm.1445.

    Article  PubMed  CAS  Google Scholar 

  • Halket, J. M., Waterman, D., Przyborowska, A. M., Patel, R. K., Fraser, P. D., & Bramley, P. M. (2005). Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. Journal of Experimental Botany, 56, 219–243. doi:10.1093/jxb/eri069.

    Article  PubMed  CAS  Google Scholar 

  • Howell, K. S., Cozzolino, D., Bartowsky, E. J., Fleet, G. H., & Henschke, P. A. (2006). Metabolic profiling as a tool for revealing Saccharomyces interactions during wine fermentation. FEMS Yeast Research, 6, 91–101. doi:10.1111/j.1567-1364.2005.00010.x.

    Article  PubMed  CAS  Google Scholar 

  • Jolliffe, I. T. (2002). Principal component analysis. New York: Springer Verlag.

    Google Scholar 

  • Josephs, J. L., & Sanders, M. (2004). Creation and comparison of MS/MS spectral libraries using quadrupole ion trap and triple-quadrupole mass spectrometers. Rapid Communications in Mass Spectrometry, 18, 743–759. doi:10.1002/rcm.1402.

    Article  PubMed  CAS  Google Scholar 

  • Kell, D. B., Brown, M., Davey, H. M., Dunn, W. B., Spasic, I., & Oliver, S. G. (2005). Metabolic footprinting and systems biology: The medium is the message. Nature Reviews. Microbiology, 3, 557–565. doi:10.1038/nrmicro1177.

    Article  PubMed  CAS  Google Scholar 

  • Matuszewski, B. K., Constanzer, M. L., & Chavez-Eng, C. M. (2003). Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS. Analytical Chemistry, 75, 3019–3030. doi:10.1021/ac020361s.

    Article  PubMed  CAS  Google Scholar 

  • McCammon, M. T. (1996). Mutants of Saccharomyces cerevisiae with defects in acetate metabolism: Isolation and characterization of Acn- mutants. Genetics, 144, 57–69.

    PubMed  CAS  Google Scholar 

  • McLafferty, F. W., & Turecek, F. (1993). Interpretation of mass spectra. Sausalito: University Science Books.

    Google Scholar 

  • Nagy, K., Takats, Z., Pollreisz, F., Szabo, T., & Vekey, K. (2003). Direct tandem mass spectrometric analysis of amino acids in dried blood spots without chemical derivatization for neonatal screening. Rapid Communications in Mass Spectrometry, 17, 983–990. doi:10.1002/rcm.1000.

    Article  PubMed  CAS  Google Scholar 

  • Nguyen, H. P., & Schug, K. A. (2008). The advantages of ESI-MS detection in conjunction with HILIC mode separations: Fundamentals and applications. Journal of Separation Science, 31, 1465–1480. doi:10.1002/jssc.200700630.

    Article  PubMed  CAS  Google Scholar 

  • Pope, G. A., MacKenzie, D. A., Defemez, M., Aroso, M. A. M. M., Fuller, L. J., Mellon, F. A., et al. (2007). Metabolic footprinting as a tool for discriminating between brewing yeasts. Yeast (Chichester, England), 24, 667–679. doi:10.1002/yea.1499.

    Article  CAS  Google Scholar 

  • Rogalewicz, F., Hoppilliard, Y., & Ohanessian, G. (2000). Fragmentation mechanisms of α-amino acids protonated under electrospray ionization: A collisional activation and ab initio theoretical study. International Journal of Mass Spectrometry, 195, 565–590. doi:10.1016/S1387-3806(99)00225-0.

    Article  Google Scholar 

  • Schauer, N., Steinhauser, D., Strelkov, S., Schomburg, D., Allison, G., Moritz, T., et al. (2005). GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Letters, 579, 1332–1337. doi:10.1016/j.febslet.2005.01.029.

    Article  PubMed  CAS  Google Scholar 

  • Stryer, L. (1995). Biochemistry. New York: W. H Freemand and Company.

    Google Scholar 

  • Taylor, P. J. (2005). Matrix effects: The Achilles heel of quantitative high-performance liquid chromatography-electrospray-tandem mass spectrometry. Clinical Biochemistry, 38, 328–334. doi:10.1016/j.clinbiochem.2004.11.007.

    Article  PubMed  CAS  Google Scholar 

  • Villas-Boas, S. G., Mas, S., Akesson, M., Smedsgaard, J., & Nielsen, J. (2005). Mass spectrometry in metabolome analysis. Mass Spectrometry Reviews, 24, 613–646. doi:10.1002/mas.20032.

    Article  PubMed  CAS  Google Scholar 

  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., & Hankemeier, T. (2007). Microbial metabolomics: Toward a platform with full metabolome coverage. Analytical Biochemistry, 370, 17–25. doi:10.1016/j.ab.2007.07.022.

    Article  PubMed  Google Scholar 

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Acknowledgements

The authors wish to thank Gerald Hofmann for fruitful discussions and comments to this manuscript.

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Authors and Affiliations

  1. Center for Microbial Biotechnology, Technical University of Denmark, Kongens Lyngby, Denmark

    Jesper Højer-Pedersen, Jørn Smedsgaard & Jens Nielsen

  2. Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden

    Jens Nielsen

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  1. Jesper Højer-Pedersen
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Correspondence to Jens Nielsen.

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Højer-Pedersen, J., Smedsgaard, J. & Nielsen, J. The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry. Metabolomics 4, 393–405 (2008). https://doi.org/10.1007/s11306-008-0132-4

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