Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species.

In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected.

[1]  Mark R. Viant,et al.  Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation , 2007, BMC Bioinformatics.

[2]  M. Klee,et al.  Method Translation and Retention Time Locking in Partition GC , 1998 .

[3]  Xin Lu,et al.  Integrated GC-MS and LC-MS plasma metabonomics analysis of ankylosing spondylitis. , 2008, The Analyst.

[4]  J. Egido,et al.  Plasma fingerprinting with GC-MS in acute coronary syndrome , 2009, Analytical and bioanalytical chemistry.

[5]  Stewart Z. Merritt.  Within-plant variation in concentrations of amino acids, sugar, and sinigrin in phloem sap of black mustard,Brassica nigra (L.) Koch (Cruciferae) , 1996, Journal of Chemical Ecology.

[6]  Johan Lindberg,et al.  A strategy for modelling dynamic responses in metabolic samples characterized by GC/MS , 2006, Metabolomics.

[7]  Carina Barth,et al.  Ascorbic acid, a familiar small molecule intertwined in the response of plants to ozone, pathogens, and the onset of senescence , 2004 .

[8]  Michael Edberg Hansen,et al.  A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants. , 2007, Biotechnology and bioengineering.

[9]  Jesús Simal-Gándara,et al.  Determination of quaternary ammonium herbicides in soils. Comparison of digestion, shaking and microwave-assisted extractions. , 2008, Journal of chromatography. A.

[10]  R. Abagyan,et al.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.

[11]  O. Fiehn,et al.  Evaluation of sampling and extraction methodologies for the global metabolic profiling of Saccharophagus degradans. , 2010, Analytical chemistry.

[12]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[13]  J. Martin-Tanguy.  Metabolism and function of polyamines in plants: recent development (new approaches) , 2001, Plant Growth Regulation.

[14]  Kishore K. Pasikanti,et al.  Gas chromatography/mass spectrometry in metabolic profiling of biological fluids. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[15]  A. Altman,et al.  Presence and identification of polyamines in xylem and Phloem exudates of plants. , 1986, Plant physiology.

[16]  Gary D. Housley,et al.  Methods in pharmacology and toxicology , 2002 .

[17]  O. Fiehn,et al.  FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. , 2009, Analytical chemistry.

[18]  M. D. De Tullio,et al.  The role of ascorbic acid in the control of flowering time and the onset of senescence. , 2006, Journal of experimental botany.

[19]  Christoph Wittmann,et al.  Metabolite profiling studies in Saccharomyces cerevisiae: an assisting tool to prioritize host targets for antiviral drug screening , 2009, Microbial cell factories.

[20]  H. E. Flores,et al.  Biochemistry and Physiology of Polyamines in Plants , 1991 .

[21]  K. Rumpel,et al.  GC-MS-Based Metabolomics , 2008 .

[22]  C. Codina,et al.  Metabolic profiling of bioactive Pancratium canariense extracts by GC-MS. , 2010, Phytochemical analysis : PCA.

[23]  O. Fiehn,et al.  Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. , 2000, Analytical chemistry.

[24]  R. Malmberg,et al.  Do Polyamines Have Roles in Plant Development , 1989 .

[25]  O. Zuloaga,et al.  Retention-time locked methods in gas chromatography. , 2009, Journal of chromatography. A.

[26]  Oliver Fiehn,et al.  Quality control for plant metabolomics: reporting MSI-compliant studies. , 2008, The Plant journal : for cell and molecular biology.

[27]  Jesús Simal-Gándara,et al.  Determination of 23 pesticide residues in leafy vegetables using gas chromatography-ion trap mass spectrometry and analyte protectants. , 2008, Journal of chromatography. A.

[28]  J. Simal-Gándara,et al.  Comparative performance of extraction strategies for polycyclic aromatic hydrocarbons in peats. , 2009, Journal of chromatography. A.

[29]  O. Beckonert,et al.  Gas chromatography/flame ionisation detection mass spectrometry for the detection of endogenous urine metabolites for metabonomic studies and its use as a complementary tool to nuclear magnetic resonance spectroscopy. , 2006, Rapid communications in mass spectrometry : RCM.

[30]  T. Hankemeier,et al.  Metabolic profiling of ultrasmall sample volumes with GC/MS: from microliter to nanoliter samples. , 2010, Analytical chemistry.

[31]  Guowang Xu,et al.  A GC-based metabonomics investigation of type 2 diabetes by organic acids metabolic profile. , 2007, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[32]  J. Simal-Gándara,et al.  Multiresidue determination of 11 new fungicides in grapes and wines by liquid-liquid extraction/clean-up and programmable temperature vaporization injection with analyte protectants/gas chromatography/ion trap mass spectrometry. , 2009, Journal of chromatography. A.