The Samuel Roberts Noble Foundation, Inc.

Sumner Group: Metabolomic References

1. Barker, D.G., Bianchi, S., Blondon, F., Dattée, Y., Duc, G., Essad, S., Flament, P., Gallusci, P., Génier, G., Pierre, G., Muel, X., Tourneur, J., Dénarié, J., Huguet, T., Medicago Truncatula, a model plant for studying the molecular genetics of the Rhizobium-Legume symbiosis, Plant Mol. Biol. Rep., 1990, 8, 40-49.

2. Cook, D.R., VandenBosch, K., de Bruijn, F.J., Huguet, T., Model legumes get the nod, Plant Cell, 1997, 275-281.

3. Cook, D.R., Medicago truncatula - a model in the making!, Curr. Opin. Plant Biol., 1999, 2, 301-304.

4. Trieu, A.T., Burleigh, S.H., Kardailsky, I.V., Maldonado-Mendoza, I.E., Versaw, W.K., Blaylock, L.A., Shin, H., Chiou, T.-J., Katagi, H., Dewbre, G.R., Weigel, D., Harrison, M.J., Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium, Plant J., 2000, 22, 531-541.

5. Bell, C.J., Dixon, R.A., Farmer, A.D., Flores, P., Inman, J., Gonzales, R.A., Harrison, M.J., Paiva, N.L., Scott, A.D., Weller, J.W., May, G.D., The Medicago genome initiative: A model legume database, Nucl. Acids Res., 2001, 29, 1-4.

6. Venter, J.C., The human genome, Science, 2001, 291, 1304-1351.

7. King, R.D., Karwath, A., Clare, A., Dehaspe, L., Accurate prediction of protein functional class from sequence in Mycobacterium tuberculosis and Escherichia coli genomes using data mining, Yeast, 2000, 17, 283-293.

8. Hieter, P., Boguski, M., Functional genomics: Its all how you read it, Science, 1997, 278, 601-602.

9. Ideker, T., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Eng, J.K., Bumgarner, R., Goodlett, D.R., Aebersold, R., Hood, L., Integrated genomic and proteomics analyses of a systematically perturbed metabolic network, Science, 2001, 292, 929-934.

10. Blackstock, W.P., Weir, M.P., Proteomics: quantitative and physical mapping of cellular protiens, Trends in Biotech., 1999, 17, 121-127.

11. Thiellement, H., Bahrman, N., Damerval, C., Plomion, C., Rossingnol, M., Santoni, V., de Vienne, D., Zivy, M., Proteomics for genetic and physiological studies in plants, Electrophoresis, 1999, 20, 2013-2026.

12. Fiehn, O., Kopka, J., Dormann, P., Altmann, T., Trethewey, R.N., Willmitzer, L., Metabolite profiling for plant functional genomics, Nature Biotechnol., 2000, 18, 1157-1161.

13. Trethewey, R.N., Krotzky, A.J., Willmitzer, L., Metabolic profiling: A Rosetta stone for genomics?, Curr. Opin. Plant Biol., 1999, 2, 83-85.

14. Trethewy, R.N., Gene discovery via metabolic profiling, Current Opin. Biotechnol., 2001, 12, 135-138.

15. Schena, M., Shalon, D., Davis, R.W., Brown, P.O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science, 1995, 270, 467-469.

16. Velculescu, V.E., Zhang, L., Vogelstein, B., Kinzlet, K.W., Serial analysis of gene expression, Science, 1995, 270, 484-487.

17. O'Farrell, P.H., High resolution two-dimensional electrophoresis of proteins, J. Biol. Chem., 1975, 250, 4007-4021.

18. Klose, J., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals, Humangenetik, 1975, 26, 231-243.

19. Klose, J., Kobalz, U., Two-dimensional electrophoresis of proteins: An updated protocol and implications for a funcitonal analysis of the genome, Electrophoresis, 1995, 16, 1034-1059.

20. Jungblut, P.R., Zimmy-Arndt, U., Zeindl-Eberhart, E., Stulik, J., Koupilova, K., Pleissner, K.P., Otto, A., Muller, E.C., Sokolowska-Kohler, W., Grabher, G., Stoffler, G., Proteomics in human disease: Cancer, heart and infectious disease, Electrophoresis, 1999, 20, 2100-2110.

21. van Wijk, K.J., Challenges and prospects of plant proteomics, Plant Physiol., 2001, 126, 501-508.

22. Morris, A.C., Djordevic, M.A., Proteome analysis of cultivar-specific interactions between Rhizobium leguminosarum biovar trifolii and subterranean clover cultivar Woogenenellup, Electrophoresis, 2001, 22, 586-598.

23. Pappin, D.J.C., Hojrup, P., Bleasby, A.J., Rapid identification of proteins by peptide-mass fingerprinting, Curr. Biol., 1993, 3, 327-332.

24. Arnott, D., O'Connell, K.L., King, K.L., Stults, J.T., An integrated approach to proteome analysis: Identification of proteins associated with cardiac hypertrophy, Anal. Biochem., 1998, 258, 1-18.

25. Yates III, J.R., Mass spectrometry and the age of the proteome, J. Am. Soc. Mass Spectrom., 1998, 33, 1-19.

26. Godovac-Zimmermann, J., Brown, L.R., Perspectives for mass spectrometry and functional proteomics, Mass Spec. Rev., 2001, 20, 1-57.

27. Conrads, T.P., Anderson, G.A., Veenstra, T.D., Pasa-Tolic, L., Smith, R.D., Utility of accurate mass tags for proteome-wide protein identification, Anal. Chem., 2000, 72, 3349-3354.

28. Clauser, K.R., Baker, P., Burlingame, A.L., Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching, Anal. Chem., 1999, 71, 2871-2882.

29. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nature Biotechnol., 1999, 17, 994-999.

30. Glassbrook, N., Beecher, C., Ryals, J., Metabolic profiling on the right path, Nature Biotechnol., 2000, 18, 1142-1143.

31. Roessner, U., Luedemann, A., Brust, D., Fiehn, O., Linke, T., Willmitzer, L., Fernie, A.R., Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems, Plant Cell, 2001, 13, 11-29.

32. Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M.C., Berden, J.A., Brindle, K.M., Kell, D.B., Rowland, J.J., Westerhoff, H.V., van Dam, K., Oliver, S.G., A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations, Nature Biotechnol., 2001, 19, 45-50.

33. Gygi, S.P., Rochon, Y., Franza, B.R., Aebersold, R., Correlation between protein and mRNA abundance in yeast, Mol. Cell. Biol., 1999, 19, 1720-1730.

34. Roessner, U., Wagner, C., Kopka, J., Trethewey, R.N., Willmitzer, L., Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry, Plant J., 2000, 23, 131-142.

35. Smith, R.D., Loo, J.A., Ogorzalek-Loo, R.R., Busman, M., Udseth, H.R., Principles and practice of electrospray ionization-mass spectrometry for large polypeptides and proteins, Mass Spec. Rev., 1991, 31, 472-485.

36. Siuzdak, G., Mass Spectrometry for Biotechnology. Academic Press, San Diego, 1996, 161 p.

37. McCloskey, J.A., Methods in Enzymology. Vol. 193: Mass Spectrometry. Academic Press, San Diego, 1990, 960 p.

38. Watson, J.T., 3rd Edition, Introduction to Mass Spectrometry. Lippincott Williams & Wilkins, New York, 1997, 512 p.

39. Katona, Z.F., Sass, P., Molnár-Perl, I., Simultaneous determination of sugars, sugar alcohols, acids, and amino acids in apricots by gas chromatography-mass spectrometry, J. Chromatogr., 1999, 847, 91-102.

40. Adams, M.A., Chen, Z., Landman, P., Colmer, T., Simultaneous determination by capillary gas chromatography of organic acids, sugars, and sugar alcohols in plant tissue extracts as their trimethylsilyl derivatives, Anal. Biochem., 1999, 266, 77-84.

41. McLafferty, F.W., Zhang, M.Y., Stauffer, D.B., Loh, S.Y., Comparison of algorithms and databases for matching unknown mass spectra, J. Am. Soc. Mass Spectrom., 1998, 9, 92-95.

42. McLafferty, F.W., Stauffer, D.A., Loh, S.Y., Wesdemiotis, C., Unknown identification using reference mass spectra. Quality evaluation of databases, J. Am. Soc. Mass Spectrom., 1999, 10, 1229-1240.

43. Pool, W.G., Leeuw, J.W., Van de Graaf, B.J., Automated extraction of pure mass spectra from gas chromatographic/mass spectrometric data, J. Mass Spectrom., 1997, 32, 438-443.

44. Halket, J.M., Przyborowska, A., Stein, S.E., Mallard, W.G., Down, S., Chalmers, R.A., Deconvolution gas chromatography/mass spectrometry of urinary organic acids--potential for patern recognition and automated identification of metabolic disorders, Rapid Commun. Mass Spectrom., 1999, 13, 279-284.

45. Herron, N.r., Donnelly, J.R., Sovocool, G.W., Software-based mass spectal enhancement to remove interferences from spectra of unknowns, J. Am. Soc. Mass Spectrom., 1996, 7, 598-604.

46. Dagan, S., Comparison of gas chromatography-pulsed flame photometric detection-mass spectrometry, automated mass spectral deconvolution and identification system and gas chromatography-tandem mass spectrometry as tools for trace level detection and identification, J. Chromatogr., A., 2000, 868, 229-247.

47. March, R.E., Todd, J.F., Practical Aspects of Ion Trap Mass Spectrometry. Vol. II, Ion Trap Instrumentation. CRC Press, Boca Raton, 1995, 320 p.

48. March, R.E., Todd, J.F., Practical Aspects of Ion Trap Mass Spectrometry. Vol I, Fundamentals of Ion Trap Mass Spectrometry., CRC Press, Boca Raton, 1995, 430 p.

49. Jennings, K.R., MS/MS instrumentation. In: Applications of Modern Mass Spectrometry in Plant Science Research (R. P. Newton and T. J. Watson, eds.), Oxford Science Publications, Oxford, 1996, pp. 25-43

50. Costello, C.E., Application of tandem mass spectral approach to structural determination of saponins. In: Advances in Experimental Medicine and Biology (G. R. Waller and K. Yamaski, eds.), 405, Plenum Publishing, New York. 1996, pp. 317-329

51. Fraser, P.D., Elisabete, M., Pinto, S., Holloway, D.E., Bramley, P.M., Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids, Plant J., 2000, 24, 551-558.

52. Silva, O., Gomes, E.T., Wolfender, J.L., Marston, A., Hostettmann, K., Application of high performance liquid chromatography coupled with ultraviolet spectroscopy and electrospray mass spectrometry to the characterisation of ellagitannins from Terminalia macroptera roots, Pharm. Res., 2000, 17, 1396-1401.

53. Waller, G.R., Jurzysta, M., Thorne, R.L.Z., Allelopathic activity of root saponins from alfalfa (Medicago sativa L.) on weeds and wheat, Bot Bull. Academy. Sin, 1993, 34, 1-11.

54. Oleszek, W., Alfalfa saponins: structure biological activity and chemotaxonomy. In: Saponins Used in Food and Agriculture; Advances in Experimental Medicine and Biology. (G. R. Waller and K. Yamasaki, eds.), Plenum Press, New York. 1996, pp. 155-170

55. Tava, A., Odoardi, M., Saponins from Medicago SPP: chemical characterization and biological activity against insects. In: Saponins Used in Food and Agriculture; Advances in Experimental Medicine and Biology. (G. R. Waller and K. Yamasaki, eds.), Vol. 405, Plenum Press, New York. 1997, pp. 97-109

56. Nagata, T., Tsushida, T., Hamaya, E., Enoki, N., Manabe, S., Nishino, C., Camellidins: Antifungal saponins isolated from Camellia japonica, Agric. Bio. Chem., 1985, 49, 1181-1186.

57. Waller, G.R., Yamasaki, K., eds., Saponins Used in Food and Agriculture; Advances in Experimental Medicine and Biology. Vol. 405, Plenum Press, New York. 1996, 441 p.

58. Jurzysta, M., Nowacki, E., Saponins of the genus Medicago, Acta Agro., 1979, 32, 13.

59. Malinow, M.P., Mac Nultry, W.P., Houghton, D.C., Kessler, S., Stenzel, P., Goodnight, S.H., Jr., Bardana, E.J., Jr., Palotay, S.L., Mac Laughlin, P., Livingston, A.L., Lack of toxicity of alfalfa saponins in Cynomolgus macaues, J. Med. Prima., 1982, 11, 106-118.

60. Haridas, V., Higuchi, M., Jayatilake, G.S., Bailey, D., Mujoo, K., Blake, M.E., Arntzen, C.J., Gutterman, J.U., Avicins: Triterpenoid saponins from Acacia victoriae (Bentham) induce apoptosis by mitochondrial perturbation, Proc. Natl. Acad. Sci., USA, 2001, 98, 5821-5826.

61. Huhman, D.V., Sumner, L.W., Metabolioc profiling of saponins in Medicago sativa and Medicago truncatula using HPLC coupled to an electrospray ion-trap mass spectometer, Phytochemistry , in press.

62. Suzuki, S., Achnine, L., Huhman, D., Sumner, L.W., Dixon, R.A., A functional genomics approach to the triterpene saponin biosynthetic pathway in Medicago truncatula. Phytochemical Society of North America, 2001, Oklahoma City, OK

63. Lide, D.R., 73rd ed., Handbook of Chemistry and Physics. (D. R. Lide, ed.), CRC Press, Boca Raton, 1992, 11-28.

64. Wehr, T., Rodriguez-Diaz, R., Liu, C.-M., Capillary electrophoresis of proteins, 1997, 37, 237-361.

65. Issaq, H.J., A decade of capillary electrophoresis, Electrophoresis, 2000, 21, 1921-1939.

66. Manabe, T., Capillary electrophoresis of proteins for proteomic studies, Electrophoresis, 1999, 20, 3116-3121.

67. Lurie, I.S., Capillary electrophoresis for drug analysis, Proc. SPIE-Int. Soc. Opt. Eng., 1999, 3576, 125-135.

68. Lagu, A.L., Applications of capillary electrophoresis in biotechnology, Electrophoresis, 1999, 20, 3145-3155.

69. Chen, S.H., Chen, Y.-H., Pharmacokinetic applications of capillary electrophoresis, Electrophoresis, 1999, 20, 3259-3268.

70. Boone, C.M., Waterval, J.C.M., Lingemann, H., Ensing, K., Underberg, W.J.M., Capillary electrophoresis as a versatile tool for the bioanalysis of drugs - a review, J. Pharm. Biomed. Anal., 1999, 20, 831-863.

71. Altria, K.D., Overview of capillary electrophoresis and capillary electrochromatograhy, J. Chromatogr., A., 1999, 856, 443-463.

72. Jorgenson, J.W., Lukacs, K.D., Zone electrophoresis in open tubular glass capillaries, Anal. Chem., 1981, 53, 1298-1302.

73. Swinney, K., Bornhop, D.J., Detection in capillary electrophoresis, Electrophoresis, 2000, 21, 1239-1250.

74. Paulus, A., Klowckow-Beck, A., Analysis of carbohydrates by capillary electrophoresis in Chromatographia: CE Series. (K. D. Altria, ed.), Vol. 3, Vieweg & Sohn, Wiesbanden, Germany, 1999, pp. 93-170.

75. El Rassi, Z., Recent developments in capillary electrophoresis and capillary electrochromatography of carbohydrate species, Electrophoresis, 1999, 20, 3134-3144.

76. Schwaiger, H., Oefner, P.J., Huber, C., Grill, E., Bonn, G.K., Capillary zone electrophoresis and micellar electrokinetic chromatography of 4-aminobenzonitrile carbohydrate, Electrophoresis, 1994, 15, 941-952.

77. Evangelista, R.A., Liu, M.-S., Chen, F.-T.A., Characterization of 9-aminopyrene-1,4,6-trisulfonate-derivatize sugars by capillary electrophoresis with laser-induced fluorescence detection, Anal. Chem., 1995, 67, 2239-2245.

78. Soga, T., Heiger, D.N., Simultaneous determination of monosaccharides in glycoproteins by capillary electrophoresis, Anal. Chem., 1998, 261, 73-83.

79. Buchberger, W., Inorganic ions. In: Handbook of Capillary Electrophoresis Applications (H. Shintani and J. Polonsky, eds.), Blackie Academic & Professional, London. 1997, pp. 531-549

80. Stover, F.S., Organic acids and organic ions. In: Handbook of Capillary Electrophoresis Applications (H. Shintani and J. Polonsky, eds.), Blackie Academic & Professional, London. 1997, pp. 550-567

81. Quirino, J.P., Terabe, S., Sample stacking of fast-moving anions in capillary zone electrophoresis, J. Chromatogr., A., 1999, 850, 339-344.

82. Yang, Y., Kang, J., Lu, H., Ou, Q., Liu, F., Determination of trace level anions in snow samples by capillary electrophoresis with sample stacking, J. Chromatogr., A., 1999, 834, 287-291.

83. Everitt, B.S., Der, G., 2nd Ed., A Handbook of Statistical Analysis Using SAS. Chapman & Hall/CRC, Boca Raton, 2001, 376 p.

84. Tabachnick, B.G., Fidell, L.S., 4th Ed., Using multivariate statistics. Allyn & Bacon, Boston, 2000, 966 p.

85. Hotellin, H., Analysis of a complex of statistical variables into principal components, J. Educ. Physchol., 1933, 24, 417-441.

86. Kohonen, T., 3rd Ed., Self-Organizing Maps. Springer, Berlin, 2000, 528 p.

87. Törönen, P., Kolehmainen, M., Wong, G., Castrén, E., Analysis of gene expression data using self-organizing maps, FEBS Lett., 1999, 451, 142-146.

88. Nikiforow, A., Schlick-Steiner, B., Steiner, F., Kalb, R., Mistrik, R., Classification of GC-MS data of epicuticular hydrocarbon from Tetramorium ants by self-organizing maps for morphological determinations. Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied topics, 2001, Chicago, IL

89. Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D., Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci., USA, 1998, 95, 14863-14868.

90. Palsson, B., The challenges of in silico biology, Nature Biotechnol., 2000, 18, 1147-1150.

91. Mendes, P., Kell, D., Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation, Bioinformatics, 1998, 14, 869-883.

92. Mendes, P., Modeling large biological systems from functional genomic data: parameter estimation. In: Foundations of Systems Biology (H. Kitano, ed.), MIT Press, Cambridge, MA. 2001, pp.

93. Voit, E.O., Radivoyevithc, T., Biochemical systems analysis of genome-wide expression data,Bioinformatics, 2000, 16, 1023-1037.