Metabolomics for unknown plant metabolites

Analytical and Bioanalytical Chemistry

Volumn 405, Issue 15, 2013, Pages 5005-5011

  Nakabayashi, Ryo ^a   Saito, Kazuki ^a,b  

^a RIKEN Plant Science Center   (Japan)

^b CHIBA UNIVERSITY   (Japan)

Author keywords

Computer assisted structure elucidation; LC MS; LC SPE NMR MS; Metabolomics; Unknown secondary metabolites

Indexed keywords

LC-MS; LC-SPE-NMR-MS; METABOLOMICS; SECONDARY METABOLITES; STRUCTURE ELUCIDATION;

MASS SPECTROMETRY; PLANTS (BOTANY);

METABOLITES;

ARABIDOPSIS; ARTICLE; CHEMICAL ANALYSIS; EQUIPMENT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METABOLOMICS; METHODOLOGY; PHYSIOLOGY;

ARABIDOPSIS; CHEMISTRY TECHNIQUES, ANALYTICAL; GENE EXPRESSION REGULATION, PLANT; METABOLOMICS;

ARABIDOPSIS THALIANA; UNIDENTIFIED PLANT;

EID: 84878317939     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-013-6869-2     Document Type: Article

References (37)

1. Hartmann T (2007) From waste products to ecochemicals: fifty years research of plant secondary metabolism. Phytochemistry 68:2831-2846
2. Newman DJ, Cragg GM (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod 75:311-335
3. Cantrell CL, Dayan FE, Duke SO (2012) Natural products as sources for new pesticides. J Nat Prod 75:1231-1242
4. Saito K, Matsuda F (2010) Metabolomics for Functional Genomics, Systems Biology, and Biotechnology. Annu Rev Plant Biol 61:463-489
5. Higashi Y, Saito K (2013) Network analysis for gene discovery in plant specialized metabolism. Plant Cell Environ. doi: 10.1111/pce.12069
6. Okazaki Y, Otsuki H, Narisawa T, Kobayashi M, Sawai S, Kamide Y, Kusano M, Aoki T, Hirai MY, Saito K (2013) A new class of plant lipid is essential for protection against phosphorus depletion. Nat Commun 4:1510
7. Fernie AR, Schauer N (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends Genet 25:39-48
8. Seki H, Sawai S, Ohyama K, Mizutani M, Ohnishi T, Sudo H, Fukushima EO, Akashi T, Aoki T, Saito K, Muranaka T (2011) Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin. Plant Cell 23:4112-4123
9. Okazaki Y, Saito K (2012) Recent advances of metabolomics in plant biotechnology. Plant Biotechnol Rep 6:1-15
10. Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G (2012) An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol 30:826-828
11. Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45:703-714
12. Sawada Y, Nakabayashi R, Yamada Y, Suzuki M, Sato M, Sakata A, Akiyama K, Sakurai T, Matsuda F, Aoki T, Hirai MY, Saito K (2012) RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database. Phytochemistry 82:38-45
13. Tohge T, Fernie AR (2009) Web-based resources for mass-spectrometry-based metabolomics: a user's guide. Phytochemistry 70:450-456
14. Neumann S, Bocker S (2010) Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules. Anal Bioanal Chem 398:2779-2788
15. Yonekura-Sakakibara K, Saito K (2009) Functional genomics for plant natural product biosynthesis. Nat Prod Rep 26:1466-1487
16. Han J, Danell RM, Patel JR, Gumerov DR, Scarlett CO, Speir JP, Parker CE, Rusyn I, Zeisel S, Borchers CH (2008) Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry. Metabolomics 4:128-140
17. Ohta D, Kanaya S, Suzuki H (2010) Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification. Curr Opin Biotechnol 21:35-44
18. Miura D, Tsuji Y, Takahashi K, Wariishi H, Saito K (2010) A strategy for the determination of the elemental composition by Fourier transform ion cyclotron resonance mass spectrometry based on isotopic peak ratios. Anal Chem 82:5887-5891
19. Kind T, Fiehn O (2010) Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev 2:23-60
20. Giavalisco P, Li Y, Matthes A, Eckhardt A, Hubberten HM, Hesse H, Segu S, Hummel J, Kohl K, Willmitzer L (2011) Elemental formula annotation of polar and lipophilic metabolites using C-13, N-15 and S-34 isotope labelling, in combination with high- resolution mass spectrometry. Plant J 68:364-376
21. Nakabayashi R, Sawada Y, Yamada Y, Suzuki M, Hirai MY, Sakurai T, Saito K (2013) Combination of liquid chromatography-fourier transform ion cyclotron resonance-mass spectrometry with (13)c-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs. Anal Chem 85:1310-1315
22. Sturm S, Seger C (2012) Liquid chromatography-nuclear magnetic resonance coupling as alternative to liquid chromatography-mass spectrometry hyphenations: Curious option or powerful and complementary routine tool? J Chromatogr A. doi: 10.1016/j.chroma.2012.05.032
23. Iwasa K, Cui WH, Sugiura M, Takeuchi A, Moriyasu M, Takeda K (2005) Structural analyses of metabolites of phenolic 1-benzyltetrahydroisoquinolines in plant cell cultures by LC/NMR, LC/MS, and LC/CD. J Nat Prod 68:992-1000
24. Tokunaga T, Okamoto M, Tanaka K, Tode C, Sugiura M (2010) Chiral Liquid Chromatography-Circular Dichroism-NMR for Estimating Separation Conditions of Chiral HPLC without Authentic Samples. Anal Chem 82:4293-4297
25. Pukalskas A, van Beek TA, de Waard P (2005) Development of a triple hyphenated HPLC-radical scavenging detection-DAD-SPE-NMR system for the rapid identification of antioxidants in complex plant extracts. J Chromatogr A 1074:81-88
26. Hendrawati O, Woerdenbag HJ, Michiels PJ, Aantjes HG, van Dam A, Kayser O (2011) Identification of lignans and related compounds in Anthriscus sylvestris by LC-ESI-MS/MS and LC-SPE-NMR. Phytochemistry 72:2172-2179
27. Staerk D, Kesting JR, Sairafianpour M, Witt M, Asili J, Emami SA, Jaroszewski JW (2009) Accelerated dereplication of crude extracts using HPLC-PDA-MS-SPE-NMR: Quinolinone alkaloids of Haplophyllum acutifolium. Phytochemistry 70:1055-1061
28. Afendi FM, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K, Ikeda S, Takahashi H, Altaf-Ul-Amin M, Darusman LK, Saito K, Kanaya S (2012) KNApSAcK Family Databases: Integrated Metabolite-Plant Species Databases for Multifaceted Plant Research. Plant Cell Physiol 53:e1
29. Sakurai T, Yamada Y, Sawada Y, Matsuda F, Akiyama K, Shinozaki K, Hirai MY, Saito K (2013) PRIMe Update: Innovative Content for Plant Metabolomics and Integration of Gene Expression and Metabolite Accumulation. Plant Cell Physiol 54:e5
30. Matsuda F, Nakabayashi R, Sawada Y, Suzuki M, Hirai MY, Kanaya S, Saito K (2011) Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity. Front Plant Sci 2:40
31. Wolf S, Schmidt S, Muller-Hannemann M, Neumann S (2010) In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinforma 11:148
32. Steinbeck C (2004) Recent developments in automated structure elucidation of natural products. Nat Prod Rep 21:512-518
33. Elyashberg ME, Williams A, Martin GE (2008) Computer-assisted structure verification and elucidation tools in NMR-based structure elucidation. Prog Nucl Magn Reson Spectrosc 53:1-104
34. Elyashberg ME, Blinov KA, Williams AJ, Molodtsov SG, Martin GE (2006) Are deterministic expert systems for computer-assisted structure elucidation obsolete? J Chem Inf Model 46:1643-1656
35. Moser A, Elyashberg ME, Williams AJ, Blinov KA, DiMartino JC (2012) Blind trials of computer-assisted structure elucidation software. J Cheminform 4:5
36. Bais HP, Vepachedu R, Gilroy S, Callaway RM, Vivanco JM (2003) Allelopathy and exotic plant invasion: From molecules and genes to species interactions. Science 301:1377-1380
37. Junker J (2011) Theoretical NMR correlations based Structure Discussion. J Cheminform 3:27