Advertisement

Resources for Metabolomics

  • Christoph BöttcherEmail author
  • Edda von Roepenack-Lahaye
  • Dierk Scheel
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 9)

Abstract

Metabolomics is developing toward an integral component of functional genomics approaches. The large structural diversity of plant metabolites requires different analytical techniques for broad metabolite analysis. In addition, new bioinformatics tools and databases are necessary for data analysis and storage. This chapter describes the resources available for comprehensive analysis of plant secondary metabolites focusing on Arabidopsis thaliana and Brassica species. In particular, a platform for non-targeted profiling of semi-polar plant metabolites based on liquid chromatography coupled to mass spectrometry is described.

Keywords

Arabidopsis thaliana Flavonoids Glucosinolates Lipids Liquid chromatography-mass spectrometry Metabolite profiling Phenylpropanoids Secondary metabolism 

Abbreviations

APCI

Atmospheric pressure chemical ionization

API

Atmospheric pressure ionization

APPI

Atmospheric pressure photoionization

CID

Collision-induced dissociation

DGDG

Digalactosyldiacylglycerol

ESI

Electrospray ionization

FT-ICR

Fourier-transform ion cyclotron resonance

GC

Gas chromatography

LC

Liquid chromatography

MS

Mass spectrometry

MGDG

Monogalactosyldiacylglycerol

NMR

Nuclear magnetic resonance

PC

Phosphatidylcholine

PE

Phosphatidylethanolamine

PG

Phosphatidylglycerol

PI

Phosphatidylinositol

ppb

Parts per billion

ppm

Parts per million

PS

Phosphatidylserine

QTOF

Quadrupole-time-of-flight

SQDG

Sulfoquinovosyldiacylglycerol

UPLC

Ultra-performance liquid chromatography

References

  1. Abdel-Farid IB, Kim HK, Choi YH, Verpoorte R (2007) Metabolic characterization of Brassica rapa leaves by NMR spectroscopy. J Agric Food Chem 55:7936–7943PubMedGoogle Scholar
  2. Abello N, Geurink PP, van der Toorn M, van Oosterhout AJM, Lugtenburg J, van der Marel GA, Kerstjens HAM, Postma DS, Overkleeft HS, Bischoff R (2008) Poly(ethylene glycol)-based stable isotope labeling reagents for the quantitative analysis of low molecular weight metabolites by LC-MS. Anal Chem 80:9171–9180PubMedGoogle Scholar
  3. Aharoni A, Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R, Goodenowe DB (2002) Nontargeted metabolome analysis by use of Fourier-transform ion cyclotron mass spectrometry. Omics 6:217–234PubMedGoogle Scholar
  4. Barry SJ, Carr RM, Lane SJ, Leavens WJ, Manning CO, Monte S, Waterhouse I (2003) Use of S-pentafluorophenyl tris(2,4,6-trimethoxyphenyl) phosphonium acetate bromide and (4-hydrazino-4-oxobutyl) [tris(2,4,6-trimethoxyphenyl)]phosphonium bromide for the derivatization of alcohols, aldehydes and ketones for detection by liquid chromatography/electrospray mass spectrometry. Rapid Commun Mass Spectrom 17:484–497PubMedGoogle Scholar
  5. Bednarek P, Schneider B, Svatos A, Oldham NJ, Hahlbrock K (2005) Structural complexity, differential response to infection, and tissue specificity of indolic and phenylpropanoid secondary metabolism in Arabidopsis roots. Plant Physiol 138:1058–1070PubMedGoogle Scholar
  6. Benton HP, Wong DM, Trauger SA, Siuzdak G (2008) XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem 80:6382–6389PubMedGoogle Scholar
  7. Bloor SJ, Abrahams S (2002) The structure of the major anthocyanin in Arabidopsis thaliana. Phytochemistry 59:343–346PubMedGoogle Scholar
  8. Bonaventure G, Salas JJ, Pollard MR, Ohlrogge JB (2003) Disruption of the FATB gene in Arabidopsis demonstrates an essential role of saturated fatty acids in plant growth. Plant Cell 15:1020–1033PubMedGoogle Scholar
  9. Böttcher C, von Roepenack-Lahaye E, Schmidt J, Clemens S, Scheel D (2009a) Analysis of phenolic choline esters from seeds of Arabidopsis thaliana and Brassica napus by capillary liquid chromatography/electrospray-tandem mass spectrometry. J Mass Spectrom 44:466–476PubMedGoogle Scholar
  10. Böttcher C, von Roepenack-Lahaye E, Schmidt J, Schmotz C, Neumann S, Scheel D, Clemens S (2008) Metabolome analysis of biosynthetic mutants reveals a diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis. Plant Physiol 147:2107–2120PubMedGoogle Scholar
  11. Böttcher C, von Roepenack-Lahaye E, Willscher E, Scheel D, Clemens S (2007) Evaluation of matrix effects in metabolite profiling based on capillary liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry. Anal Chem 79:1507–1513PubMedGoogle Scholar
  12. Böttcher C, Westphal L, Schmotz C, Prade E, Scheel D, Glawischnig E (2009b) The multifunctional enzyme CYP71B15 (PHYTOALEXIN DEFICIENT3) converts cysteine-indole-3-acetonitrile to camalexin in the indole-3-acetonitrile metabolic network of Arabidopsis thaliana. Plant Cell 21:1830–1845PubMedGoogle Scholar
  13. Bouchereau A, Hamelin J, Lamour I, Renard M, Larher F (1991) Distribution of sinapine and related compounds in seeds of Brassica and allied genera. Phytochemistry 30:1873–1881Google Scholar
  14. Bringmann G, Kajahn I, Neususs C, Pelzing M, Laug S, Unger M, Holzgrabe U (2005) Analysis of the glucosinolate pattern of Arabidopsis thaliana seeds by capillary zone electrophoresis coupled to electrospray ionization-mass spectrometry. Electrophoresis 26:1513–1522PubMedGoogle Scholar
  15. Broadhurst DI, Kell DB (2006) Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics 2:171–196Google Scholar
  16. Brown PD, Tokuhisa JG, Reichelt M, Gershenzon J (2003) Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana. Phytochemistry 62:471–481PubMedGoogle Scholar
  17. Browse J, Somerville CR (1994) Glycerolipids. In: Meyerowitz EM, Somerville CR (eds) Arabidopsis, pp 881–912. Cold Spring Harbor Laboratory Press, Cold Spring HaborGoogle Scholar
  18. Carlson EE, Cravatt BF (2007a) Chemoselective probes for metabolite enrichment and profiling. Nat Methods 4:429–435PubMedGoogle Scholar
  19. Carlson EE, Cravatt BF (2007b) Enrichment tags for enhanced-resolution profiling of the polar metabolome. J Am Chem Soc 129:15780–15782PubMedGoogle Scholar
  20. Cataldi TRI, Rubino A, Lelario F, Bufo SA (2007) Naturally occurring glucosinolates in plant extracts of rocket salad (Eruca sativa L.) identified by liquid chromatography coupled with negative ion electrospray ionization and quadrupole ion-trap mass spectrometry. Rapid Commun Mass Spectrom 21:2374–2388PubMedGoogle Scholar
  21. Catchpole GS, Beckmann M, Enot DP, Mondhe M, Zywicki B, Taylor J, Hardy N, Smith A, King RD, Kell DB, Fiehn O, Draper J (2005) Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc Natl Acad Sci U S A 102:14458–14462PubMedGoogle Scholar
  22. Chapple CCS, Shirely BW, Zook M, Hammerschmidt R, Somerville SC (1994) Secondary metabolism in Arabidopsis. In: Meyerowitz EM, Somerville CR (eds) Arabidopsis, pp 989–1030. Cold Spring Harbor Laboratory Press, Cold Spring HaborGoogle Scholar
  23. Chen F, Tholl D, D’Auria JC, Farooq A, Pichersky E, Gershenzon J (2003) Biosynthesis and emission of terpenoid volatiles from Arabidopsis flowers. Plant Cell 15:481–494PubMedGoogle Scholar
  24. Chernushevich IV, Loboda AV, Thomson BA (2001) An introduction to quadrupole-time-of-flight mass spectrometry. J Mass Spectrom 36:849–865PubMedGoogle Scholar
  25. Cuyckens F, Claeys M (2004) Mass spectrometry in the structural analysis of flavonoids. J Mass Spectrom 39:1–15PubMedGoogle Scholar
  26. De Vos RC, Moco S, Lommen A, Keurentjes JJ, Bino RJ, Hall RD (2007) Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc 2:778–791PubMedGoogle Scholar
  27. Devaiah SP, Roth MR, Baughman E, Li MY, Tamura P, Jeannotte R, Welti R, Wang XM (2006) Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a PHOSPHOLIPASE D alpha 1 knockout mutant. Phytochemistry 67:1907–1924PubMedGoogle Scholar
  28. Dixon RA, Xie DY, Sharma SB (2005) Proanthocyanidins - a final frontier in flavonoid research? New Phytol 165:9–28PubMedGoogle Scholar
  29. Dunn WB (2008) Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes. Phys Biol 5. doi:10.1088/1478–3975/5/1/011001PubMedGoogle Scholar
  30. D’Auria JC, Gershenzon J (2005) The secondary metabolism of Arabidopsis thaliana: growing like a weed. Curr Opin Plant Biol 8:308–316PubMedGoogle Scholar
  31. Farmer EE, Almeras E, Krishnamurthy V (2003) Jasmonates and related oxylipins in plant responses to pathogenesis and herbivory. Curr Opin Plant Biol 6:372–378PubMedGoogle Scholar
  32. Fellenberg C, Milkowski C, Hause B, Lange PR, Bottcher C, Schmidt J, Vogt T (2008) Tapetum-specific location of a cation-dependent O-methyltransferase in Arabidopsis thaliana. Plant J 56:132–145PubMedGoogle Scholar
  33. Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L (2004) Metabolite profiling: from diagnostics to systems biology. Nat Rev Mol Cell Biol 5:763–769PubMedGoogle Scholar
  34. Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18:1157–1161PubMedGoogle Scholar
  35. Fiehn O, Sumner LW, Rhee SY, Ward J, Dickerson J, Lange BM, Lane G, Roessner U, Last R, Nikolau B (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics 3:195–201Google Scholar
  36. Fu J, Keurentjes JJB, Bouwmeester H, America T, Verstappen FWA, Ward JL, Beale MH, de Vos RCH, Dijkstra M, Scheltema RA, Johannes F, Koornneef M, Vreugdenhil D, Breitling R, Jansen RC (2009) System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat Genet 41:166–167PubMedGoogle Scholar
  37. Gangl ET, Annan M, Spooner N, Vouros P (2001) Reduction of signal suppression effects in ESI-MS using a nanosplitting device. Anal Chem 73:5635–5644PubMedGoogle Scholar
  38. Giavalisco P, Hummel J, Lisec J, Inostroza AC, Catchpole G, Willmitzer L (2008) High-resolution direct infusion-based mass spectrometry in combination with whole 13C metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. Anal Chem 80:9417–9425PubMedGoogle Scholar
  39. Giavalisco P, Kohl K, Hummel J, Seiwert B, Willmitzer L (2009) 13C Isotope-labeled metabolomes allowing for improved compound annotation and relative quantification in liquid chromatography-mass spectrometry-based metabolomic research. Anal Chem 81:6546–6551PubMedGoogle Scholar
  40. Glauser G, Grata E, Dubugnon L, Rudaz S, Farmer EE, Wolfender JL (2008a) Spatial and temporal dynamics of jasmonate synthesis and accumulation in Arabidopsis in response to wounding. J Biol Chem 283:16400–16407PubMedGoogle Scholar
  41. Glauser G, Guillarme D, Grata E, Boccard J, Thiocone A, Carrupt PA, Veuthey JL, Rudaz S, Wolfender JL (2008b) Optimized liquid chromatography-mass spectrometry approach for the isolation of minor stress biomarkers in plant extracts and their identification by capillary nuclear magnetic resonance. J Chromatogr A 1180:90–98PubMedGoogle Scholar
  42. Grange AH, Zumwalt MC, Sovocool GW (2006) Determination of ion and neutral loss compositions and deconvolution of product ion mass spectra using an orthogonal acceleration time-of-flight mass spectrometer and an ion correlation program. Rapid Commun Mass Spectrom 20:89–102PubMedGoogle Scholar
  43. Grata E, Boccard J, Guillarme D, Glauser G, Carrupt PA, Farmer EE, Wolfender JL, Rudaz S (2008) UPLC-TOF-MS for plant metabolomics: a sequential approach for wound marker analysis in Arabidopsis thaliana. J Chromatogr B Analyt Technol Biomed Life Sci 871:261–270PubMedGoogle Scholar
  44. Grata E, Guillarme D, Glauser G, Boccard J, Carrupt PA, Veuthey JL, Rudaz S, Wolfender JL (2009) Metabolite profiling of plant extracts by ultra-high-pressure liquid chromatography at elevated temperature coupled to time-of-flight mass spectrometry. J Chromatogr A 1216:5660–5668PubMedGoogle Scholar
  45. Hagemeier J, Schneider B, Oldham NJ, Hahlbrock K (2001) Accumulation of soluble and wall-bound indolic metabolites in Arabidopsis thaliana leaves infected with virulent or avirulent Pseudomonas syringae pathovar tomato strains. Proc Natl Acad Sci U S A 98:753–758PubMedGoogle Scholar
  46. Harrabi S, Herchi W, Kallel H, Mayer PM, Boukhchina S (2009) Liquid chromatographic-mass spectrometric analysis of glycerophospholipids in corn oil. Food Chem 114:712–716Google Scholar
  47. Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR (2007) Stable isotope assisted assignment of elemental compositions for metabolomics. Anal Chem 79:6912–6921PubMedGoogle Scholar
  48. Hill DW, Kertesz TM, Fontaine D, Friedman R, Grant DF (2008) Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra. Anal Chem 80:5574–5582PubMedGoogle Scholar
  49. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280:25590–25595PubMedGoogle Scholar
  50. Hopley C, Bristow T, Lubben A, Simpson A, Bul E, Klagkou K, Herniman J, Langley J (2008) Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers. Rapid Commun Mass Spectrom 22:1779–1786PubMedGoogle Scholar
  51. Huhman DV, Sumner LW (2002) Metabolic profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectrometer. Phytochemistry 59:347–360PubMedGoogle Scholar
  52. Isaac G, Jeannotte R, Esch SW, Welti R (2007) New mass-spectrometry-based strategies for lipids. Genet Eng (N Y) 28:129–157Google Scholar
  53. Kachlicki P, Einhorn J, Muth D, Kerhoas L, Stobiecki M (2008) Evaluation of glycosylation and malonylation patterns in flavonoid glycosides during LC/MS/MS metabolite profiling. J Mass Spectrom 43:572–586PubMedGoogle Scholar
  54. Kai K, Mizutani M, Kawamura N, Yamamoto R, Tamai M, Yamaguchi H, Sakata K, Shimizu B (2008) Scopoletin is biosynthesized via ortho-hydroxylation of feruloyl CoA by a 2-oxoglutarate-dependent dioxygenase in Arabidopsis thaliana. Plant J 55:989–999PubMedGoogle Scholar
  55. Kai K, Shimizu B, Mizutani M, Watanabe K, Sakata K (2006) Accumulation of coumarins in Arabidopsis thaliana. Phytochemistry 67:379–386PubMedGoogle Scholar
  56. Katajamaa M, Miettinen J, Oresic M (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22:634–636PubMedGoogle Scholar
  57. Katajamaa M, Oresic M (2005) Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6. doi:10.1186/1471–2105–6–179PubMedGoogle Scholar
  58. Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN (2005) On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci U S A 102:4252–4257PubMedGoogle Scholar
  59. Kerhoas L, Aouak D, Cingoz A, Routaboul JM, Lepiniec L, Einhorn J, Birlirakis N (2006) Structural characterization of the major flavonoid glycosides from Arabidopsis thaliana seeds. J Agric Food Chem 54:6603–6612PubMedGoogle Scholar
  60. Keurentjes JJB, Koornneef M, Vreugdenhil D (2008) Quantitative genetics in the age of omics. Curr Opin Plant Biol 11:123–128PubMedGoogle Scholar
  61. Kind T, Fiehn O (2006) Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 7. doi:10.1186/1471–2105–7–234PubMedGoogle Scholar
  62. Kind T, Fiehn O (2007) Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8. doi:10.1186/1471–2105–8–105PubMedGoogle Scholar
  63. Kliebenstein DJ (2004) Secondary metabolites and plant/environment interactions: a view through Arabidopsis thaliana tinged glasses. Plant Cell Environ 27:675–684Google Scholar
  64. Konishi Y, Kiyota T, Draghici C, Gao JM, Yeboah F, Acoca S, Jarussophon S, Purisima E (2007) Molecular formula analysis by an MS/MS/MS technique to expedite dereplication of natural products. Anal Chem 79:1187–1197PubMedGoogle Scholar
  65. Lamos SM, Shortreed MR, Frey BL, Belshaw PJ, Smith LM (2007) Relative quantification of carboxylic acid metabolites by liquid chromatography-mass spectrometry using isotopic variants of cholamine. Anal Chem 79:5143–5149PubMedGoogle Scholar
  66. Last RL, Jones AD, Shachar-Hill Y (2007) Towards the plant metabolome and beyond. Nat Rev Mol Cell Biol 8:167–174PubMedGoogle Scholar
  67. Leavens WJ, Lane SJ, Carr RM, Lockie AM, Waterhouse I (2002) Derivatization for liquid chromatography/electrospray mass spectrometry: synthesis of tris(trimethoxyphenyl)phosphonium compounds and their derivatives of amine and carboxylic acids. Rapid Commun Mass Spectrom 16:433–441PubMedGoogle Scholar
  68. Li Y, Beisson F, Pollard M, Ohlrogge J (2006) Oil content of Arabidopsis seeds: the influence of seed anatomy, light and plant-to-plant variation. Phytochemistry 67:904–915PubMedGoogle Scholar
  69. Li HJ, Deinzer ML (2007) Tandem mass spectrometry for sequencing proanthocyanidins. Anal Chem 79:1739–1748PubMedGoogle Scholar
  70. Lommen A (2009) MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 81:3079–3086PubMedGoogle Scholar
  71. Luo J, Fuell C, Parr A, Hill L, Bailey P, Elliott K, Fairhurst SA, Martin C, Michael AJ (2009) A novel polyamine acyltransferase responsible for the accumulation of spermidine conjugates in Arabidopsis seed. Plant Cell 21:318–333PubMedGoogle Scholar
  72. Malitsky S, Blum E, Less H, Venger I, Elbaz M, Morin S, Eshed Y, Aharoni A (2008) The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators. Plant Physiol 148:2021–2049PubMedGoogle Scholar
  73. Matsuda F, Yonekura-Sakakibara K, Niida R, Kuromori T, Shinozaki K, Saito K (2009) MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J 57:555–577PubMedGoogle Scholar
  74. Mellon FA, Bennett RN, Holst B, Williamson G (2002) Intact glucosinolate analysis in plant extracts by programmed cone voltage electrospray LC/MS: performance and comparison with LC/MS/MS methods. Anal Biochem 306:83–91PubMedGoogle Scholar
  75. Meyer RC, Steinfath M, Lisec J, Becher M, Witucka-Wall H, Törjék O, Fiehn O, Eckardt Ä, Willmitzer L, Selbig J, Altmann T (2007) The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc Natl Acad Sci U S A 104:4759–4764PubMedGoogle Scholar
  76. Mock HP, Wray V, Beck W, Metzger JW, Strack D (1993) Coumaroylaspartate from cell-suspension cultures of Arabidopsis thaliana. Phytochemistry 34:157–159Google Scholar
  77. Moco S, Schneider B, Vervoort J (2009) Plant micrometabolomics: the analysis of endogenous metabolites present in a plant cell or tissue. J Proteome Res 8:1694–1703PubMedGoogle Scholar
  78. Muroi A, Ishihara A, Tanaka C, Ishizuka A, Takabayashi J, Miyoshi H, Nishioka T (2009) Accumulation of hydroxycinnamic acid amides induced by pathogen infection and identification of agmatine coumaroyltransferase in Arabidopsis thaliana . Planta 230:517–527PubMedGoogle Scholar
  79. Neue UD, Mazzeo JR (2001) A theoretical study of the optimization of gradients at elevated temperature. J Sep Sci 24:921–929Google Scholar
  80. Nordstrom A, Want E, Northen T, Lehtio J, Siuzdak G (2008) Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics. Anal Chem 80:421–429PubMedGoogle Scholar
  81. Ohta D, Shibata D, Kanaya S (2007) Metabolic profiling using Fourier-transform ion-cyclotron-resonance mass spectrometry. Anal Bioanal Chem 389:1469–1475PubMedGoogle Scholar
  82. Ojanpera S, Pelander A, Pelzing M, Krebs I, Vuori E, Ojanpera I (2006) Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 20:1161–1167PubMedGoogle Scholar
  83. Oksman-Caldentey KM, Saito K (2005) Integrating genomics and metabolomics for engineering plant metabolic pathways. Curr Opin Biotechnol 16:174–179PubMedGoogle Scholar
  84. Pauwels L, Morreel K, De Witte E, Lammertyn F, Van Montagu M, Boerjan W, Inze D, Goossens A (2008) Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells. Proc Natl Acad Sci U S A 105:1380–1385PubMedGoogle Scholar
  85. Pedras MS, Adio AM, Suchy M, Okinyo DP, Zheng QA, Jha M, Sarwar MG (2006) Detection, characterization and identification of crucifer phytoalexins using high-performance liquid chromatography with diode array detection and electrospray ionization mass spectrometry. J Chromatogr A 1133:172–183PubMedGoogle Scholar
  86. Pedras MS, Okanga FI, Zaharia IL, Khan AQ (2000) Phytoalexins from crucifers: synthesis, biosynthesis, and biotransformation. Phytochemistry 53:161–176PubMedGoogle Scholar
  87. Pellegrin V (1983) Molecular formulas of organic compounds-the nitrogen rule and degree of unsaturation. J Chem Educ 60:626–633Google Scholar
  88. Petersen BL, Chen SX, Hansen CH, Olsen CE, Halkier BA (2002) Composition and content of glucosinolates in developing Arabidopsis thaliana. Planta 214:562–571PubMedGoogle Scholar
  89. Reichelt M, Brown PD, Schneider B, Oldham NJ, Stauber E, Tokuhisa J, Kliebenstein DJ, Mitchell-Olds T, Gershenzon J (2002) Benzoic acid glucosinolate esters and other glucosinolates from Arabidopsis thaliana. Phytochemistry 59:663–671PubMedGoogle Scholar
  90. Roberts LD, McCombie G, Titman CM, Griffin JL (2008) A matter of fat: an introduction to lipidomic profiling methods. J Chromatogr B Analyt Technol Biomed Life Sci 871:174–181PubMedGoogle Scholar
  91. Rochfort SJ, Trenerry VC, Imsic M, Panozzo J, Jones R (2008) Class targeted metabolomics: ESI ion trap screening methods for glucosinolates based on MSn fragmentation. Phytochemistry 69:1671–1679PubMedGoogle Scholar
  92. Rohde A, Morreel K, Ralph J, Goeminne G, Hostyn V, De Rycke R, Kushnir S, Van Doorsselaere J, Joseleau JP, Vuylsteke M, Van Driessche G, Van Beeumen J, Messens E, Boerjan W (2004) Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. Plant Cell 16:2749–2771PubMedGoogle Scholar
  93. Routaboul JM, Kerhoas L, Debeaujon I, Pourcel L, Caboche M, Einhorn J, Lepiniec L (2006) Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana. Planta 224:96–107PubMedGoogle Scholar
  94. Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics - ‘majority report by precogs’. Trends Plant Sci 13:36–43PubMedGoogle Scholar
  95. Schmidt A, Karas M, Dulcks T (2003) Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI? J Am Soc Mass Spectrom 14:492–500PubMedGoogle Scholar
  96. Scholz M, Gatzek S, Sterling A, Fiehn O, Selbig J (2004) Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20:2447–2454PubMedGoogle Scholar
  97. Scholz M, Selbig J (2007) Visualization and analysis of molecular data. In: Weckwerth W (ed) Metabolomics: methods and protocols, pp 87–104. Humana Press, Totowa, NJGoogle Scholar
  98. Schwab W (2003) Metabolome diversity: too few genes, too many metabolites? Phytochemistry 62:837–649PubMedGoogle Scholar
  99. Shepherd T, Dobson G, Verrall SR, Conner S, Griffiths DW, McNicol JW, Davies HV, Stewart D (2007) Potato metabolomics by GC-MS: what are the limiting factors? Metabolomics 3:475–488Google Scholar
  100. Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78:779–787PubMedGoogle Scholar
  101. Steeghs M, Bais HP, de Gouw J, Goldan P, Kuster W, Northway M, Fall R, Vivanco JM (2004) Proton-transfer-reaction mass spectrometry as a new tool for real time analysis of root-secreted volatile organic compounds in Arabidopsis. Plant Physiol 135:47–58PubMedGoogle Scholar
  102. Steuer R, Morgenthal K, Weckwerth W, Selbig J (2007) A gentle guide to the analysis of metabolomic data. In: Weckwerth W (ed) Metabolomics: Methods and Protocols, pp 105–126. Humana Press, Totowa, NJGoogle Scholar
  103. Stobiecki M, Skirycz A, Kerhoas L, Kachlicki P, Muth D, Einhorn J, Mueller-Roeber B (2006) Profiling of phenolic glycosidic conjugates in leaves of Arabidopsis thaliana using LC/MS. Metabolomics 2:197–219Google Scholar
  104. Stoll N, Schmidt E, Thurow K (2006) Isotope pattern evaluation for the reduction of elemental compositions assigned to high-resolution mass spectral data from electrospray ionization fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 17:1692–1699PubMedGoogle Scholar
  105. Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O (2008) OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 9. doi:10.1186/1471–2105–9–163PubMedGoogle Scholar
  106. Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, Daykin CA, Fan TWM, Fiehn O, Goodacre R, Griffin JL, Hankemeier T, Hardy N, Harnly J, Higashi R, Kopka J, Lane AN, Lindon JC, Marriott P, Nicholls AW, Reily MD, Thaden JJ, Viant MR (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3:211–221Google Scholar
  107. Sysi-Aho M, Katajamaa M, Yetukuri L, Oresic M (2007) Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8. doi:10.1186/1471–2105–8–93PubMedGoogle Scholar
  108. t’Kindt R, De Veylder L, Storme M, Deforce D, Van Bocxlaer J (2008) LC-MS metabolic profiling of Arabidopsis thaliana plant leaves and cell cultures: optimization of pre-LC-MS procedure parameters. J Chromatogr B Analyt Technol Biomed Life Sci 871:37–43PubMedGoogle Scholar
  109. Tan J, Bednarek P, Liu J, Schneider B, Svatos A, Hahlbrock K (2004) Universally occurring phenylpropanoid and species-specific indolic metabolites in infected and uninfected Arabidopsis thaliana roots and leaves. Phytochemistry 65:691–699PubMedGoogle Scholar
  110. Tautenhahn R, Bottcher C, Neumann S (2008) Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics 9. doi:10.1186/1471–2105–9–504Google Scholar
  111. Tautenhahn R, Böttcher C, Neumann S (2007) Annotation of LC/ESI-MS mass signals. In: Hochreiter S (ed) Bioinformatics and research and development, pp 371–380. Springer, HeidelbergGoogle Scholar
  112. Thiocone A, Farmer EE, Wolfender JL (2008) Screening for wound-induced oxylipins in Arabidopsis thaliana by differential HPLC-APCI/MS profiling of crude leaf extracts and subsequent characterisation by capillary-scale NMR. Phytochem Anal 19:198–205PubMedGoogle Scholar
  113. Tholl D, Chen F, Petri J, Gershenzon J, Pichersky E (2005) Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J 42:757–771PubMedGoogle Scholar
  114. Tian QG, Rosselot RA, Schwartz SJ (2005) Quantitative determination of intact glucosinolates in broccoli, broccoli sprouts, brussels sprouts, and cauliflower by high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. Anal Biochem 343:93–99PubMedGoogle Scholar
  115. Tohge T, Fernie AR (2009) Web-based resources for mass-spectrometry-based metabolomics: a user’s guide. Phytochemistry 70:450–456PubMedGoogle Scholar
  116. Tohge T, Nishiyama Y, Hirai MY, Yano M, Nakajima J, Awazuhara M, Inoue E, Takahashi H, Goodenowe DB, Kitayama M, Noji M, Yamazaki M, Saito K (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J 42:218–235PubMedGoogle Scholar
  117. Tomer KB, Moseley MA, Deterding LJ, Parker CE (1994) Capillary liquid-chromatography mass-spectrometry. Mass Spectrom Rev 13:431–457Google Scholar
  118. Tsuji J, Jackson EP, Gage DA, Hammerschmidt R, Somerville SC (1992) Phytoalexin accumulation in Arabidopsis thaliana during the hypersensitive reaction to Pseudomonas syringae pv syringae. Plant Physiol 98:1304–1309PubMedGoogle Scholar
  119. van den Berg RA, Hoefsloot HC, Westerhuis JA, Smilde AK, van der Werf MJ (2006) Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7. doi:10.1186/1471–2164–7–142PubMedGoogle Scholar
  120. Veit M, Pauli GF (1999) Major flavonoids from Arabidopsis thaliana leaves. J Nat Prod 62:1301–1303PubMedGoogle Scholar
  121. von Roepenack-Lahaye E, Degenkolb T, Zerjeski M, Franz M, Roth U, Wessjohann L, Schmidt J, Scheel D, Clemens S (2004) Profiling of Arabidopsis secondary metabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry. Plant Physiol 134:548–559Google Scholar
  122. Wallis JG, Browse J (2002) Mutants of Arabidopsis reveal many roles for membrane lipids. Prog Lipid Res 41:254–278PubMedGoogle Scholar
  123. Wang X (2002) Phospholipase D in hormonal and stress signaling. Curr Opin Plant Biol 5:408–414PubMedGoogle Scholar
  124. Ward JL, Harris C, Lewis J, Beale MH (2003) Assessment of 1H NMR spectroscopy and multivariate analysis as a technique for metabolite fingerprinting of Arabidopsis thaliana. Phytochemistry 62:949–957PubMedGoogle Scholar
  125. Welti R, Wang X (2004) Lipid species profiling: a high-throughput approach to identify lipid compositional changes and determine the function of genes involved in lipid metabolism and signaling. Curr Opin Plant Biol 7:337–344PubMedGoogle Scholar
  126. Werner E, Croixmarie V, Umbdenstock T, Ezan E, Chaminade P, Tabet JC, Junot C (2008a) Mass spectrometry-based metabolomics: accelerating the characterization of discriminating signals by combining statistical correlations and ultrahigh resolution. Anal Chem 80:4918–4932PubMedGoogle Scholar
  127. Werner E, Heilier JF, Ducruix C, Ezan E, Junot C, Tabet JC (2008b) Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends. J Chromatogr B Analyt Technol Biomed Life Sci 871:143–163PubMedGoogle Scholar
  128. Wolfender JL, Waridel P, Ndjoko K, Hobby KR, Major HJ, Hostettmann K (2000) Evaluation of Q-TOF-MS/MS and multiple stage IT-MSn for the dereplication of flavonoids and related compounds in crude plant extracts. Analusis 28:895–906Google Scholar
  129. Yang WC, Adamec J, Regnier FE (2007) Enhancement of the LC/MS analysis of fatty acids through derivatization and stable isotope coding. Anal Chem 79:5150–5157PubMedGoogle Scholar
  130. Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20:2160–2176PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Christoph Böttcher
    • 1
    Email author
  • Edda von Roepenack-Lahaye
    • 1
  • Dierk Scheel
    • 1
  1. 1.Department of Stress and Developmental BiologyLeibniz Institute of Plant BiochemistryHalle/SaaleGermany

Personalised recommendations