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MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites

By Fumio Matsuda, Keiko Yonekura-Sakakibara, Rie Niida, Takashi Kuromori, Kazuo Shinozaki and Kazuki Saito


The MS/MS spectral tag (MS2T) library-based peak annotation procedure was developed for informative non-targeted metabolic profiling analysis using LC-MS. An MS2T library of Arabidopsis metabolites was created from a set of MS/MS spectra acquired using the automatic data acquisition function of the mass spectrometer. By using this library, we obtained structural information for the detected peaks in the metabolic profile data without performing additional MS/MS analysis; this was achieved by searching for the corresponding MS2T accession in the library. In the case of metabolic profile data for Arabidopsis tissues containing more than 1000 peaks, approximately 50% of the peaks were tagged by MS2Ts, and 90 peaks were identified or tentatively annotated with metabolite information by searching the metabolite databases and manually interpreting the MS2Ts. A comparison of metabolic profiles among the Arabidopsis tissues revealed that many unknown metabolites accumulated in a tissue-specific manner, some of which were deduced to be unusual Arabidopsis metabolites based on the MS2T data. Candidate genes responsible for these biosyntheses could be predicted by projecting the results to the transcriptome data. The method was also used for metabolic phenotyping of a subset of Ds transposon-inserted lines of Arabidopsis, resulting in clarification of the functions of reported genes involved in glycosylation of flavonoids. Thus, non-targeted metabolic profiling analysis using MS2T annotation methods could prove to be useful for investigating novel functions of secondary metabolites in plants

Topics: Technical Advance
Publisher: Blackwell Publishing Ltd
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Provided by: PubMed Central

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  23. (2005). Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor.
  24. (2006). Gas chromatography mass spectrometry-based metabolite profiling in plants.
  25. (2008). Gene expression and metabolism in tomato fruit surface tissues.
  26. (2001). Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants.
  27. (2008). High-throughput, nontargeted metabolite fingerprinting using nominal mass flow injection electrospray mass spectrometry.
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  29. (1986). Hydroxycinnamic acid spermidine amides from pollen of Corylus avellena L.
  30. (2003). Identification and characterization of plant agmatine iminohydrolase, the last missing link in polyamine biosynthesis of plants.
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  32. (2007). Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics.
  33. (2002). Jasmonate-induced changes in flavonoid metabolism in barley (Hordeum vulgare) leaves.
  34. (2006). KNApSAcK: a comprehensive species–metabolite relationship database.
  35. (2008). Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends.
  36. (2005). Mass spectrometry in metabolome analysis.
  37. (2007). Mass spectrometry-based metabolomics.
  38. (2006). Metabolic changes in Arabidopsis thaliana expressing the feedback-resistant anthranilate synthase a subunit gene OASA1D.
  39. (2007). Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry.
  40. (2005). Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism.
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  42. (2007). Metabolite profiling of mycorrhizal roots of Medicago truncatula.
  43. (2008). Metabolome analysis of biosynthetic mutants reveals diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis thaliana.
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  46. (2007). Metabolomics technologies and metabolite identification.
  47. (2009). MS/MS spectral tag-based LC-MS metabolomics 575 ª 2008 The Authors Journal compilation ª 2008 Blackwell Publishing Ltd, The Plant Journal,
  48. (2008). MS/MS spectral tag-based LC-MS metabolomics 577 ª
  49. (2001). N,N¢,N¢¢-triferuloylspermidine, a new UV absorbing polyamine derivative from pollen of Hippeastrum x hortorum.
  50. (2007). Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis.
  51. (2008). Optimized liquid chromatography-mass spectrometry approach for the isolation of minor stress biomarkers in plant extracts and their identification by capillary nuclear magnetic resonance.
  52. (2007). Phytochemical genomics in Arabidopsis thaliana: a case study for functional identification of flavonoid biosynthesis genes.
  53. (2004). Potential of metabolomics as a functional genomics tool.
  54. (2006). Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data-a potential toolformulti-parametricdiagnosis.J.ProteomeRes.5,1407–1414.
  55. (2003). Preparation and biological assessment of hydroxycinnamic acid amides of polyamines.
  56. (2005). Processing methods for differential analysis of LC/MS profile data.
  57. (2004). Profiling ofArabidopsis secondarymetabolites by capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry.
  58. (2005). Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry.
  59. (2003). Purification, cloning and properties of an acyltransferase controlling shikimate and quinate ester intermediate in phenylpropanoid metabolism.
  60. (2007). Rapid classification of phenotypic mutants of Arabidopsis via metabolite fingerprinting.
  61. (2005). Silencing nature’s narcotics: metabolic engineering of the opium poppy.
  62. (2004). Silencing of hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyltransferase affects phenylpropanoid biosynthesis.
  63. (1998). Structural analyses and dynamics of soluble and cell wall-bound phenolics in a broad spectrum resistance to the powdery mildew fungus in barley.
  64. (2008). The Authors Journal compilation ª 2008 Blackwell Publishing Ltd, The Plant Journal,
  65. (1984). The biosynthesis of feruloyltyramine in Nicotiana tabacum.
  66. (1978). The distribution of hydroxycinnamic acid amides in flowering plants.
  67. (2003). The diverse bacterial origins of the Arabidopsis polyamine biosynthetic pathway.
  68. (2007). The hyper-fluorescent trichome phenotype of the brt1 mutant of Arabidopsis is the result of a defect in a sinapic acid:-UDPG glucosyltransferase.
  69. (2008). The role of UDP-glucose:hydroxycinnamate glucosyltransferases in phenylpropanoid metabolism and the response to UV-B radiation in Arabidopsis thaliana.
  70. (2006). Thegenetics ofplantmetabolism.Nat.
  71. (2007). Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment.
  72. (2006). TM4 microarray software suite.
  73. (2003). TM4: a free, opensource system for microarray data management and analysis.
  74. (2008). Towards de novo identification of metabolites by analyzing tandem mass spectra.
  75. (2003). UGT73C6 and UGT78D1, glycosyltransferases involved in flavonol glycoside biosynthesis in Arabidopsis thaliana.
  76. (2007). Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry.
  77. (2008). UPLC-TOF-MS for plant metabolomics: a sequential approach for wound marker analysis in Arabidopsis thaliana.
  78. (2003). Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana.
  79. (2008). Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models.
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