Skip to main content
Book cover

Plant Metabolomics pp 3–20Cite as

Gas Chromatography Mass Spectrometry

  • Chapter

Part of the Biotechnology in Agriculture and Forestry book series (AGRICULTURE,volume 57)

Keywords

  • Matrix Assisted Laser Desorption Ionization
  • Mass Fragment
  • Curr Opin Plant Biol
  • Quantify Mass
  • Mass Isotopomers

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/3-540-29782-0_1
  • Chapter length: 18 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   229.00
Price excludes VAT (USA)
  • ISBN: 978-3-540-29782-6
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   299.99
Price excludes VAT (USA)
Hardcover Book
USD   349.99
Price excludes VAT (USA)
Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Ausloos P, Clifton CL, Lias SG, Mikaya AI, Stein SE, Tchekhovskoi DV, Sparkman OD, Zaikin V, Zhu D (1999) The critical evaluation of a comprehensive mass spectral library. J Am Soc Mass Spectrom 10:287–299

    PubMed  CAS  CrossRef  Google Scholar 

  • Barsch A, Patschkowski T, Niehaus K (2004) Comprehensive metabolite profiling of Sinorhizobium meliloti using gas chromatography-mass spectrometry. Funct Integrat Genomics 4:219–230

    CAS  Google Scholar 

  • Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9:418–425

    PubMed  CAS  CrossRef  Google Scholar 

  • Birkemeyer C, Kolasa A, Kopka J (2003) Comprehensive chemical derivatization for gas chromatography-mass spectrometry-based multi-targeted profiling of the major phytohormones. J Chromatogr A 993:89–102

    PubMed  CAS  CrossRef  Google Scholar 

  • Birkemeyer C, Luedemann A, Wagner C, Erban A, Kopka J (2005) Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling. Trends Biotechnol 23:28–33

    PubMed  CAS  CrossRef  Google Scholar 

  • Blau K, Halket JM (1993) Handbook of derivatives for chromatography, 2nd edn. Wiley, New York

    Google Scholar 

  • Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW (2005) Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. J Exp Bot 56:323–336

    PubMed  CAS  CrossRef  Google Scholar 

  • Colebatch G, Desbrosses G, Ott T, Krusell L, Kloska S, Kopka J, Udvardi MK (2004) Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J 39:487–512

    PubMed  CrossRef  Google Scholar 

  • Cook D, Fowler S, Fiehn O, Thomashow MF (2004) A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci USA 101:15243–15248

    PubMed  CAS  CrossRef  Google Scholar 

  • Desbrosses G, Kopka J, Udvardi MK (2005) Legume metabolomics: development of GC-MS resources for functional genomics of plant-microbe interactions. Plant Physiol 137:1302–1318

    PubMed  CAS  CrossRef  Google Scholar 

  • Duran AL, Yang J, Wang L, Sumner LW (2003) Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics 19:2283–2293

    PubMed  CAS  CrossRef  Google Scholar 

  • Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L (2004) Metabolite profiling: from diagnostics to systems biology. Nat Rev Mol Cell Biol 5:763–769

    PubMed  CAS  CrossRef  Google Scholar 

  • Fiehn O (2002) Metabolomics — the link between genotypes and phenotypes. Plant Mol Biol 48:155–171

    PubMed  CAS  CrossRef  Google Scholar 

  • Fiehn O (2003) Metabolic networks of Cucurbita maxima phloem. Phytochem 62:875–86

    CAS  CrossRef  Google Scholar 

  • Fiehn O, Kopka J, Trethewey RN, Willmitzer L (2000a) Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal Chem 72:3573–3580

    PubMed  CAS  CrossRef  Google Scholar 

  • Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN, Willmitzer L (2000b) Metabolite profiling for plant functional genomics. Nat Biotechnol 18:1157–1161

    PubMed  CAS  CrossRef  Google Scholar 

  • Fischer E, Sauer U (2003) Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem 270:880–891

    PubMed  CAS  CrossRef  Google Scholar 

  • Gullberg J, Jonsson P, Nordström A, Sjöström M, Moritz T (2004) Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331:283–295

    PubMed  CAS  CrossRef  Google Scholar 

  • Halket JM, Przyborowska A, Stein SE, Mallard WG, Down S, Chalmers RA (1999) Deconvolution gas chromatography mass spectrometry of urinary organic acids — potential for pattern recognition and automated identification of metabolic disorders. Rapid Commun Mass Spectrom 13:279–284

    PubMed  CAS  CrossRef  Google Scholar 

  • Halket JM, Waterman D, Przyborowska AM, Patel RKP, Fraser PD, Bramley PM (2005) Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J Exp Bot 56:219–243

    PubMed  CAS  CrossRef  Google Scholar 

  • Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall RD, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee S, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wang T, Walsh S, Wurtele ES, Kell DB (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnol 22:1601–1606

    CAS  CrossRef  Google Scholar 

  • Jonsson P, Gullberg J, Nordström A, Kusano M, Kowalczyk M, Sjöström M, Moritz T (2004) A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Anal Chem 76:1738–1745

    PubMed  CAS  CrossRef  Google Scholar 

  • Jonsson P, Johansson AI, Gullberg J, Trygg J, A J, Grung B, Marklund S, Sjostrom M, Antti H, Moritz T (2005) High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Anal Chem 77: 5635–5642

    PubMed  CAS  CrossRef  Google Scholar 

  • Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, Sung DY, Guy CL (2004) Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol 136:4159–4168

    PubMed  CAS  CrossRef  Google Scholar 

  • Knapp DR (1979) Handbook of analytical derivatization reactions. Wiley, New York

    Google Scholar 

  • Kopka J, Fernie AF, Weckwerth W, Gibon Y, Stitt M (2004) Metabolite profiling in Plant Biology: Platforms and Destinations. Genome Biol 5(6):109–117

    PubMed  CrossRef  Google Scholar 

  • Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmüller E, Dörmann P, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D (2005) GMD@CSBDB: The Golm Metabolome Database. Bioinformatics 21:1635–1638

    PubMed  CAS  CrossRef  Google Scholar 

  • Kovàts ES (1958) Gas-chromatographische Charakterisierung organischer Verbindungen: Teil 1. Retentionsindices aliphatischer Halogenide, Alkohole, Aldehyde und Ketone. Helv Chim Acta 41:1915–1932

    CrossRef  Google Scholar 

  • Little JL (1999) Artifacts in trimethylsilyl derivatization reactions and ways to avoid them. J Chromatorgr A 844:1–22

    CAS  CrossRef  Google Scholar 

  • Mashego MR, Wu L, van Dam JC, Ras C, Vinke JL, van Winden WA, van Gulik WM, Heijnen JJ (2004) MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotech Bioeng 85:620–628

    CAS  CrossRef  Google Scholar 

  • Mueller A, Duechting P, Weiler EW (2002) A multiplex GC-MS/MS technique for the sensitive and quantitative single-run analysis of acidic phytohormones and related compounds, and its application to Arabidopsis thaliana. Planta 216:44–56

    CrossRef  Google Scholar 

  • Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L (2000) Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23:131–142

    PubMed  CAS  CrossRef  Google Scholar 

  • Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR (2001a) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13:11–29

    PubMed  CAS  CrossRef  Google Scholar 

  • Roessner U, Willmitzer L, Fernie AR (2001b) High-resolution metabolic phenotyping of genetically and environmentally diverse plant systems — identification of phenocopies. Plant Physiol 127:749–764

    PubMed  CAS  CrossRef  Google Scholar 

  • Roessner U, Willmitzer L, Fernie AR (2002) Metabolic profiling and biochemical phenotyping of plant systems. Plant Cell Rep 21:189–196

    CAS  CrossRef  Google Scholar 

  • Roessner-Tunali U, Hegemann B, Lytovchenko A, Carrari F, Bruedigam C, Granot D, Fernie AR (2003) Metabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phosphorylation diminishes during fruit development. Plant Physiol 133:84–99

    PubMed  CAS  CrossRef  Google Scholar 

  • Roessner-Tunali U, Lui J, Leisse A, Balbo I, Perez-Melis A, Willmitzer L, Fernie AR (2004) Flux analysis of organic and amino acid metabolism in potato tubers by gas chromatography-mass spectrometry following incubation in 13C labelled isotopes. Plant J 39:668–679

    PubMed  CAS  CrossRef  Google Scholar 

  • Ryan D, Shellie R, Tranchida P, Casilli A, Mondello L, Marriott P (2004) Analysis of roasted coffee bean volatiles by using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. J Chromatogr A 1054:57–65

    PubMed  CAS  CrossRef  Google Scholar 

  • Sauer U (2004) High-throughput phenomics: experimental methods for mapping fluxomes. Curr Opin Biotechnol 15:58–63

    PubMed  CAS  CrossRef  Google Scholar 

  • Sauter H, Lauer M, Fritsch H (1988) Metabolite profiling of plants — a new diagnostic technique. Abstr Pap Am Chem Soc 195:129

    Google Scholar 

  • Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, Lundgren K, Roessner-Tunali U, Forbes MG, Willmitzer L, Fernie AR, Kopka J (2005) GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett 579:1332–1337

    PubMed  CAS  CrossRef  Google Scholar 

  • Schmelz EA, Engelberth J, Alborn HT, O’Donnell P, Sammons M, Toshima H, Tumlinson JH (2003) Simultaneous analysis of phytohormones, phytotoxins, and volatile organic compounds in plants. Proc Natl Acad Sci USA 100:10552–10557

    PubMed  CAS  CrossRef  Google Scholar 

  • Schmelz EA, Engelberth J, Tumlinson JH, Block A, Alborn HT (2004) The use of vapor phase extraction in metabolic profiling of phytohormones and other metabolites. Plant J 39:790–808

    PubMed  CAS  CrossRef  Google Scholar 

  • Shao XG, Wang GQ, Wang SF, Su QD (2004) Extraction of mass spectra and chromatographic profiles from overlapping GC/MS signal with background. Anal Chem 76:5143–5148

    PubMed  CAS  CrossRef  Google Scholar 

  • Sinha AE, Fraga CG, Prazen BJ, Synovec RE (2004a) Trilinear chemometric analysis of twodimensional comprehensive gas chromatography-time-of-flight mass spectrometry data. J Chromatogr A 1027:269–277

    PubMed  CAS  CrossRef  Google Scholar 

  • Sinha AE, Hope JL, Prazen BJ, Nilsson EJ, Jack RM, Synovec RE (2004b) Algorithm for locating analytes of interest based on mass spectral similarity in GC×GC-TOF-MS data: analysis of metabolites in human infant urine. J Chromatogr. A 1058:209–215

    PubMed  CAS  CrossRef  Google Scholar 

  • Sinha AE, Prazen BJ, Synovec RE (2004c) Trends in chemometric analysis of comprehensive two-dimensional separations. Anal Bioanal Chem 378:1948–1951

    PubMed  CAS  CrossRef  Google Scholar 

  • Stein SE (1999) An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J Am Soc Mass Spectrom 10:770–781

    CAS  CrossRef  Google Scholar 

  • Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20:3647–3651

    PubMed  CAS  CrossRef  Google Scholar 

  • Stephanopoulos G, Alper H, Moxley J (2004) Exploiting biological complexity for strain improvement through systems biology. Nat Biotechnol 22:1261–1267

    PubMed  CAS  CrossRef  Google Scholar 

  • Strelkov S, von Elstermann M, Schomburg D (2004) Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol Chem 385:853–861

    PubMed  CAS  CrossRef  Google Scholar 

  • Sumner LW, Mendes P, Dixon RA (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62:817–836

    PubMed  CAS  CrossRef  Google Scholar 

  • Toyo’oka T (1999) Modern derivatization methods for separation science. Wiley, New York

    Google Scholar 

  • Trethewey RN (2004) Metabolite profiling as an aid to metabolic engineering in plants. Curr Opin Plant Biol 7:196–201

    PubMed  CAS  CrossRef  Google Scholar 

  • Trethewey RN, Krotzky AJ, Willmitzer L (1999) Metabolic profiling: a Rosetta stone for genomics? Curr Opin Plant Biol 2:83–85

    PubMed  CAS  CrossRef  Google Scholar 

  • Urbanczyk-Wochniak E, Fernie AR (2005) Metabolic profiling reveals altered nitrogen nutrient regimes have diverse effects on the metabolism of hydroponically-grown tomato (Solanum lycopersicum) plants. J Exp Bot 56:309–321

    PubMed  CAS  CrossRef  Google Scholar 

  • Urbanczyk-Wochniak E, Luedemann A, Kopka J, Selbig J, Roessner-Tunali U, Willmitzer L, Fernie AR (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Reports 4:989–993

    PubMed  CAS  CrossRef  Google Scholar 

  • Van Deursen MM, Beens J, Janssen HG, Leclercq PA, Cramers CA (2000) Evaluation of time-of-flight mass spectrometric detection for fast gas chromatography. J Chromatogr A 878:205–213

    CrossRef  Google Scholar 

  • Veriotti T, Sacks R (2001) High-speed GC and GC/time-of-flight MS of lemon and lime oil samples. Anal Chem 73:4395–4402

    PubMed  CAS  CrossRef  Google Scholar 

  • Vreuls RJJ, Dallüge J, Brinkman UAT (1999) Gas chromatography — time-of-flight mass spectrometry for sensitive determination of organic microcontaminants. J Microcolumn Sep 11:663–675

    CAS  CrossRef  Google Scholar 

  • Wagner C, Sefkow M, Kopka J (2003)Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochem 62:887–900

    CAS  CrossRef  Google Scholar 

  • Weckwerth W, Loureiro ME, Wenzel K, Fiehn O (2004a) Differential metabolic networks unravel the effects of silent plant phenotypes. Proc Natl Acad Sci USA 18:7809–7814

    CrossRef  Google Scholar 

  • Weckwerth W, Wenzel K, Fiehn O (2004b) Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4:78–83

    PubMed  CAS  CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany

    J. Kopka

Authors
  1. J. Kopka
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba, 263-8522, Japan

    Professor Dr. Kazuki Saito

  2. RIKEN Plant Science Center, Yokohama, 230-0045, Japan

    Professor Dr. Kazuki Saito

  3. Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

    Professor Dr. Richard A. Dixon

  4. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Golm, Germany

    Professor Dr. Lothar Willmitzer

Rights and permissions

Reprints and Permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Kopka, J. (2006). Gas Chromatography Mass Spectrometry. In: Saito, K., Dixon, R.A., Willmitzer, L. (eds) Plant Metabolomics. Biotechnology in Agriculture and Forestry, vol 57. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-29782-0_1

Download citation