Web-based resources for mass-spectrometry-based metabolomics: A user's guide

Phytochemistry

Volumn 70, Issue 4, 2009, Pages 450-456

  Tohge, Takayuki ^a   Fernie, Alisdair R ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

Bioinformatics; GC MS; LC MS; Metabolomics; Peak alignment; Peak identification; Web resource

Indexed keywords

BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; INTERNET; LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; METABOLISM; METABOLOMICS; METHODOLOGY; PLANT; SHORT SURVEY;

CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; INTERNET; MASS SPECTROMETRY; METABOLOMICS; PLANTS; SOFTWARE;

EID: 62549159971     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2009.02.004     Document Type: Short Survey

References (86)

1. Adams, R.P., 2007. Identification of Essential Oil Components by Gas Chromatography-Quadrupole Mass Spectroscopy, 4th ed. Allured Pub Corp, Carol Stream, IL, USA.
2. Aharoni A., Ric de Vos C.H., Verhoeven H.A., Maliepaard C.A., Kruppa G., Bino R., and Goodenowe D.B. Nontargeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry. OMICS 6 (2003) 217-234
3. Arita, M., 2008. A pitfall of wiki solution for biological databases, Brief. Bioinform. (Epub ahead of print).
4. Arita M., and Suwa K. Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database. BioData Min. 17 (2008) 1-8
5. Ausloos P., Clifton C.L., Lias S.G., Mikaya A.I., Stein S.E., Tchekhovskoi D.V., Sparkman O.D., Zaikin V., and Zhu D. The critical evaluation of a comprehensive mass spectral library. J. Am. Soc. Mass Spectrom. 10 (1999) 287-299
6. Benton H.P., Wong D.M., Trauger S.A., and Siuzdak G. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal. Chem. 80 (2008) 6382-6389
7. Caspi R., Foerster H., Fulcher C.A., Kaipa P., Krummenacker M., Latendresse M., Paley S., Rhee S.Y., Shearer A.G., Tissier C., Walk T.C., Zhang P., and Karp P.D. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 36 (2008) D623-D631
8. Chen J., Swamidass S.J., Dou Y., Bruand J., and Baldi P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics 21 (2005) 4133-4139
9. Chen J.H., Linstead E., Swamidass S.J., Wang D., and Baldi P. ChemDB update - full-text search and virtual chemical space. Bioinformatics 23 (2007) 2348-2351
10. Cui Q., Lewis I.A., Hegeman A.D., Anderson M.E., Li J., Schulte C.F., Westler W.M., Eghbalnia H.R., Sussman M.R., and Markley J.L. Metabolite identification via the Madison Metabolomics Consortium Database. Nat. Biotechnol. 26 (2008) 162-164
11. De Luca V., and St Pierre B. The cell and developmental biology of alkaloid biosynthesis. Trends Plant Sci. 5 (2000) 168-173
12. De Vos R.C., Moco S., Lommen A., Keurentjes J.J., Bino R.J., and Hall R.D. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat. Protoc. 2 (2007) 778-791
13. Degtyarenko K., de Matos P., Ennis M., Hastings J., Zbinden M., McNaught A., Alcántara R., Darsow M., Guedj M., and Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36 (2008) D344-D350
14. Desbrosses G.G., Kopka J., and Udvardi M.K. Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiol. 137 (2005) 1302-1318
15. Duran A.L., Yang J., Wang L.J., and Sumner L.W. Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics 19 (2003) 2283-2293
16. Ebbels T.M., Keun H.C., Beckonert O.P., Bollard M.E., Lindon J.C., Holmes E., and Nicholson J.K. Prediction and classification of drug toxicity using probabilistic modeling of temporal metabolic data: the consortium on metabonomic toxicology screening approach. J. Proteome Res. 6 (2007) 4407-4422
17. Fahy E., Subramaniam S., Brown H.A., Glass C.K., Merrill A.H., Murphy R.C., Raetz C.R., Russell D.W., Seyama Y., Shaw W., Shimizu T., Spener F., van Meer G., VanNieuwenhze M.S., White S.H., Witztum J.L., and Dennis E.A. A comprehensive classification system for lipids. J. Lipid Res. 46 (2005) 839-861
18. Fernie A.R. The future of metabolic phytochemistry: larger numbers of metabolites, higher resolution, greater understanding. Phytochemistry 68 (2007) 2861-2880
19. Fernie A.R., and Schauer N. Metabolomics-assisted breeding: a viable option for crop improvement?. Trends Genet. 25 (2009) 39-48
20. Fernie A.R., Trethewey R.N., Krotzky A.J., and Willmitzer L. Metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell. Biol. 5 (2004) 763-769
21. Fiehn O. Metabolomics - the link between genotype and phenotype. Plant Mol. Biol. 48 (2002) 155-171
22. Fiehn O. Metabolic networks of Cucurbita maxima phloem. Phytochemistry 62 (2003) 875-886
23. Fiehn O., Kopka J., Dörmann P., Altmann T., Trethewey R.N., and Willmitzer L. Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18 (2000) 1157-1161
24. Fiehn O., Wohlgemuth G., and Scholz M. Setup and annotation of metabolomic experiments by integrating biological and mass spectrometric metadata. Proc. Lect. Note Bioinform. 3615 (2005) 224-239
25. Fiehn O., Wohlgemuth G., Scholz M., Kind T., Lee do Y., Lu Y., Moon S., and Nikolau B. Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J. 53 (2008) 691-704
26. Giavalisco P., Hummel J., Lisec J., Inostroza A.C., Catchpole G., and Willmitzer L. High-resolution direct infusion-based mass spectrometry in combination with whole (13)c metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. Anal. Chem. 15 (2008) 9417-9425
27. Grafahrend-Belau E., Weise S., Koschützki D., Scholz U., Junker B.H., and Schreiber F. MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 36 (2008) D954-D958
28. Halket J.M., Waterman D., Przyborowska A.M., Patel R.K., Fraser P.D., and Bramley P.M. Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J. Exp. Bot. 56 (2005) 219-243
29. Hanhineva K., Rogachev I., Kokko H., Mintz-Oron S., Venger I., Kärenlampi S., and Aharoni A. Non-targeted analysis of spatial metabolite composition in strawberry (Fragariaxananassa) flowers. Phytochemistry 69 (2008) 2463-2481
30. Hirai M.Y., Yano M., Goodenowe D.B., Kanaya S., Kimura T., Awazuhara M., Arita M., Fujiwara T., and Saito K. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 101 (2004) 10205-10210
31. Holmes E., and Antti H. Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological NMR spectra. Analyst 127 (2002) 1549-1557
32. Horai H., Arita M., and Nishioka T. Comparison of ESI-MS spectra in MassBank database. Proc. Int. Conf. Biomed. Eng. Inform. 2 (2008) 853-857
33. Huege J., Sulpice R., Gibon Y., Lisec J., Koehl K., and Kopka J. GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13CO2 labelling. Phytochemistry 68 (2007) 2258-2272
34. Hummel, J., Selbig, J., Walther, D., Kopka, J., 2008. The Golm Metabolome Database: a database for GC-MS based metabolite profiling. In: Hohmann, S. (Ed.) Topics in Current Genetics: Nielsen, J., Jewett, M. (Eds.) Metabolomics. Springer-Verlag, Berlin, Heidelberg, New York.
35. Iijima Y., Nakamura Y., Ogata Y., Tanaka K., Sakurai N., Suda K., Suzuki T., Suzuki H., Okazaki K., Kitayama M., Kanaya S., Aoki K., and Shibata D. Metabolite annotations based on the integration of mass spectral information. Plant J. 54 (2008) 949-962
36. Jenkins H., Hardy N., Beckmann M., Draper J., Smith A.R., Taylor J., Fiehn O., Goodacre R., Bino R.J., Hall R., Kopka J., Lane G.A., Lange B.M., Liu J.R., Mendes P., Nikolau B.J., Oliver S.G., Paton N.W., Rhee S., Roessner-Tunali U., Saito K., Smedsgaard J., Sumner L.W., Wang T., Walsh S., Wurtele E.S., and Kell D.B. A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol. 22 (2004) 1601-1606
37. Kanehisa M., and Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28 (2000) 27-30
38. Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., Katayama T., Araki M., and Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34 (2006) D354-D357
39. Karp P.D., Ouzounis C.A., Moore-Kochlacs C., Goldovsky L., Kaipa P., Ahrén D., Tsoka S., Darzentas N., Kunin V., and López-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33 (2005) 6083-6089
40. Karp P.D., Keseler I.M., Shearer A., Latendresse M., Krummenacker M., Paley S.M., Paulsen I., Collado-Vides J., Gama-Castro S., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola M.I., Bonavides-Martinez C., and Ingraham J. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 35 (2007) 7577-7590
41. Katajamaa M., and Oresic M. Processing software for differential analysis of LC/MS profile data. BMC Bioinform. 6 (2005) 179.1-179.12
42. Kind T., and Fiehn O. Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. BMC Bioinform. 7 (2006) 234
43. Kind T., and Fiehn O. Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinform. 8 (2007) 115
44. Kopka J., Schauer N., Krueger S., Birkemeyer C., Usadel B., Bergmüller E., Dörmann P., Weckwerth W., Gibon Y., Stitt M., Willmitzer L., Fernie A.R., and Steinhauser D. GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 21 (2005) 1635-1638
45. Linstrom P.J., and Mallard W.G. The NIST Chemistry WebBook: a chemical data resource on the internet. J. Chem. Eng. Data 46 (2001) 1059-1063
46. Lisec J., Schauer N., Kopka J., Willmitzer L., and Fernie A.R. Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat. Protoc. 1 (2006) 387-396
47. Luedemann A., Strassburg K., Erban A., and Kopka J. TagFinder for the quantitative analysis of gas chromatography-mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics 24 (2008) 732-737
48. Masciocchi J., Frau G., Fanton M., Sturlese M., Floris M., Pireddu L., Palla P., Cedrati F., Rodriguez-Tomé P., and Moro S. MMsINC: a large-scale chemoinformatics database. Nucleic Acids Res. 37 (2009) D284-D290
49. Matsuda, F., Yonekura-Sakakibara, K., Niida, R., Kuromori, T., Shinozaki, K., Saito, K., 2008. MS/MS spectral tag (MS2T)-based annotation of non-targeted profile of plant secondary metabolites. Plant J. (Epub ahead of print).
50. McLafferty F.W., Zhang M.Y., Stauffer D.B., and Loh S.Y. Comparison of algorithms and databases for matching unknown mass spectra. J. Am. Soc. Mass Spectrom. 1 (1998) 92-95
51. Moco S., Bino R.J., Vorst O., Verhoeven H.A., de Groot J., van Beek T.A., Vervoort J., and de Vos C.H. A liquid chromatography mass spectrometry based Metabolome Database for Tomato. Plant Physiol. 141 (2006) 1205-1218
52. Morikawa T., Mizutani M., Aoki N., Watanabe B., Saga H., Saito S., Oikawa A., Suzuki H., Sakurai N., Shibata D., Wadano A., Sakata K., and Ohta D. Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato. Plant Cell 18 (2006) 1008-1022
53. Mueller L.A., Zhang P., and Rhee S.Y. AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 132 (2003) 453-460
54. Nobeli I., and Thornton J.M. A bioinformatician's view of the metabolome. Bioessays 28 (2006) 534-545
55. Nobeli I., Ponstingl H., Krissinel E.B., and Thornton J.M. A structure-based anatomy of the E. coli metabolome. J. Mol. Biol. 334 (2003) 697-719
56. Ohta D., Shibata D., and Kanaya S. Metabolic profiling using Fourier-transform ion-cyclotron-resonance mass spectrometry. Anal. Bioanal. Chem. 389 (2007) 1469-1475
57. Oikawa A., Nakamura Y., Ogura T., Kimura A., Suzuki H., Sakurai N., Shinbo Y., Shibata D., Kanaya S., and Ohta D. Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiol. 142 (2006) 398-413
58. Oksman-Caldentey K.M., and Saito K. Integrating genomics and metabolomics for engineering plant metabolic pathways. Curr. Opin. Biotechnol. 16 (2005) 174-179
59. Ott M.A., and Vriend G. Correcting ligands, metabolites, and pathways. BMC Bioinform. 7 (2006) 517
60. Petersen B.L., Chen S., Hansen C.H., Olsen C.E., and Halkier B.A. Composition and content of glucosinolates in developing Arabidopsis thaliana. Planta 214 (2002) 562-571
61. Rosania G.R., Crippen G., Woolf P., States D., and Shedden K. A cheminformatic toolkit for mining biomedical knowledge. Pharm. Res. 24 (2007) 1791-1802
62. Schauer N., and Fernie A.R. Plant metabolomics: towards biological function and mechanism. Trends Plant Sci. 11 (2006) 508-516
63. Schauer N., Steinhauser D., Strelkov S., Schomburg D., Allison G., Moritz T., Lundgren K., Roessner-Tunali U., Forbes M.G., Willmitzer L., Fernie A.R., and Kopka J. GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett. 579 (2005) 1332-1337
64. Schauer N., Zamir D., and Fernie A.R. Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J. Exp. Bot. 56 (2005) 297-307
65. Shinbo Y., Nakamura Y., Altaf-Ul-Amin M., Asahi H., Kurokawa K., Arita M., Saito K., Ohta D., Shibata D., and Kanaya S. KNApSAcK: a comprehensive species-metabolite relationship database. Biotechnol. Agr. Forest. 57 (2006) 166-181
66. Smith R.M., and Busch K.L. Understanding Mass Spectra - A Basic Approach (1999), Wiley
67. Smith C.A., O'Maille G., Want E.J., Qin C., Trauger S.A., Brandon T.R., Custodio D.E., Abagyan R., and Siuzdak G. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27 (2005) 747-751
68. Smith C.A., Want E.J., O'Maille G., Abagyan R., and Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78 (2006) 779-787
69. Stein S.E. An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J. Am. Soc. Mass Spectrom. 10 (1999) 770-781
70. Stein S.E., and Scott D.R. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5 (1994) 859-866
71. Steinfath M., Groth D., Lisec J., and Selbig J. Metabolite profile analysis: from raw data to regression and classification. Physiol. Plant. 132 (2008) 150-161
72. Steinhauser D., Usadel B., Luedemann A., Thimm O., and Kopka J. GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics 21 (2005) 1635-1638
73. Strehmel N., Hummel J., Erban A., Strassburg K., and Kopka J. Retention index thresholds for compound matching in GC-MS metabolite profiling. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 871 (2008) 182-190
74. Suhre K., and Schmitt-Kopplin P. MassTRIX: Mass TRanslator Into Pathways. Nucleic Acids Res. 36 (2008) W481-W484
75. Sumner L.W., Mendes P., and Dixon R.A. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62 (2003) 817-836
76. Takahashi H., Kai K., Shinbo Y., Tanaka K., Ohta D., Oshima T., Altaf-Ul-Amin M., Kurokawa K., Ogasawara N., and Kanaya S. Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry. Anal. Bioanal. Chem. 391 (2008) 2769-2782
77. Thimm O., Bläsing O., Gibon Y., Nagel A., Meyer S., Krüger P., Selbig J., Müller L.A., Rhee S.Y., and Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37 (2004) 914-939
78. Tohge T., Nishiyama Y., Yokota Hirai M., Yano M., Nakajima J., Awazuhara M., Inoue E., Takahashi H., Goodenowe D.B., Kitayama M., Noji M., Yamazaki M., and Saito K. Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. Plant J. 42 (2005) 218-235
79. Tokimatsu T., Sakurai N., Suzuki H., Ohta H., Nishitani K., Koyama T., Umezawa T., Misawa N., Saito K., and Shibata D. KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol. 138 (2005) 1289-1300
80. Vorst O.F.J., Vos C.H.d., Lommen A., Staps R.V., Visser R.G.F., Bino R.J., and Hall R.D. A non-directed approach to the differential analysis of multiple LC-MS-derived metabolic profiles. Metabolomics 1 (2005) 169-180
81. Wagner C., Sefkow M., and Kopka J. Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry 62 (2003) 887-900
82. Watanabe K., Yasug E., and Oshima M. How to search the glycolipid data in LIPIDBANK for Web: the newly developed lipid database. Trend Glycosci. Glycotechnol. 12 (2000) 175-184
83. Wiklund S., Johansson E., Sjostrom L., Mellerowicz E.J., Edlund U., Shockcor J.P., Gottfries J., Moritz T., and Trygg J. Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models. Anal. Chem. 80 (2008) 115-122
84. Wishart D.S., Tzur D., Knox C., Eisner R., Guo A.C., Young N., Cheng D., Jewell K., Arndt D., Sawhney S., Fung C., Nikolai L., Lewis M., Coutouly M.A., Forsythe I., Tang P., Shrivastava S., Jeroncic K., Stothard P., Amegbey G., Block D., Hau D.D., Wagner J., Miniaci J., Clements M., Gebremedhin M., Guo N., Zhang Y., Duggan G.E., Macinnis G.D., Weljie A.M., Dowlatabadi R., Bamforth F., Clive D., Greiner R., Li L., Marrie T., Sykes B.D., Vogel H.J., and Querengesser L. HMDB: the Human Metabolome Database. Nucleic Acids Res. 35 (2007) D521-D526
85. Yonekura-Sakakibara K., Tohge T., Matsuda F., Nakabayashi R., Takayama H., Niida R., Watanabe-Takahashi A., Inoue E., and Saito K. Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20 (2008) 2160-2176
86. Zhang P., Foerster H., Tissier C.P., Mueller L., Paley S., Karp P.D., and Rhee S.Y. MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol. 138 (2005) 27-37