Mass spectrometry methods in metabolomics

Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry

Volumn 3, Issue 1, 2009, Pages 1-9

  Lokhov, P G ^a   Archakov, A I ^a  

^a INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

Author keywords

Mass spectrometry; Metabolic fingerprinting; Metabolic profiling; Metabolomics

Indexed keywords

ANGIOTENSIN; CHOLESTEROL; CITRIC ACID; CREATININE; CYANOCOBALAMIN; GLUTAMIC ACID; INOSITOL; LYSINE; METHIONINE; PALMITIC ACID; PHENYLALANINE; PROLINE; TRYPTOPHAN; UREA;

ACCURACY; ANALYTIC METHOD; CAPILLARY ELECTROPHORESIS; CONCENTRATION RESPONSE; ELECTROSPRAY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; LIPID ANALYSIS; LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; METABOLIC FINGERPRINTING; METABOLIC PROFILING; METABOLITE; METABOLOME; METABOLOMICS; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN DETERMINATION; REVIEW; SENSITIVITY AND SPECIFICITY;

EID: 63349093096     PISSN: 19907508     EISSN: 19907516     Source Type: Journal    
DOI: 10.1134/S1990750809010016     Document Type: Review

References (79)

1. Vigneau-Callahan, K.E., Shestopalov, A.I., Milbury, P.E., Matson, W.R., and Kristal, B.S., J. Nutr., 2001, vol. 131, pp. 924-932.
2. Bino, R.J., Hall, R.D., Fiehn, O., Kopka, J., Saito, K., Draper, J., Nikolau, B.J., Mendes, P., Roessner-Tunali, U., Beale, M.H., Trethewey, R.N., Lange, B.M., Wurtele, E.S., and Sumner, L.W., Trends Plant Sci., 2004, vol. 9, pp. 418-425.
3. Beecher, C.W.W., in: Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, George, G. and Harrigan, R.G., Eds., New York: Springer, 2003 pp. 311-335.
4. Weckwerth, W., Annu. Rev. Plant. Biol., 2003, vol. 54, pp. 669-689.
5. Dettmer, K. and Hammock, B.D., Environ. Health Perspect., 2004, vol. 112, pp. 396-397.
6. Smedsgaard, J. and Frisvad, J.C., J. Microbiol. Meth., 1996, vol. 25, pp. 5-17.
7. Smedsgaard, J. and Frisvad, J.C., Biochem. Syst. Ecol., 1997, vol. 25, pp. 51-64.
8. Castrillo, J.I., Hayes, A., Mohammed, S., Gaskell, S.J., and Oliver, S.G., Phytochemistry, 2003, vol. 62, pp. 929-937.
9. Allen, J., Davey, H.M., Broadhurst, D., Heald, J.K., Rowland, J.J., Oliver, S.G., and Kell, D.B., Nat. Biotechnol., 2003, vol. 21, pp. 692-696.
10. Allen, J., Davey, H.M., Broadhurst, D., Rowland, J.J., Oliver, S.G., and Kell, D.B., Appl. Environ. Microbiol., 2004, vol. 70, pp. 6157-6165.
11. Scholz, M., Gatzek, S., Sterling, A., Fiehn, O., and Selbig, J., Bioinformatics, 2004, vol. 20, pp. 2447-2454.
12. Vaidyanathan, S., Kell, D.B., and Goodacre, R., J. Am. Soc. Mass Spectrom., 2002, vol. 13, pp. 118-128.
13. Marshall, A.G., Hendrickson, C.L., and Jackson, G.S., Mass Spectrom. Rev., 1998, vol. 17, pp. 1-35.
14. Brown, S.C., Kruppa, G., and Dasseux, J.L., Mass Spectrom. Rev., 2005, vol. 24, pp. 223-231.
15. Aharoni, A., Ric de Vos, C.H., Verhoeven, H.A., Maliepaard, C.A., Kruppa, G., Bino, R., and Goodenowe, D.B., Omics, 2002, vol. 6, pp. 217-234.
16. Hirai, M.Y., Yano, M., Goodenowe, D.B., Kanaya, S., Kimura, T., Awazuhara, M., Arita, M., Fujiwara, T., and Saito, K., Proc. Natl. Acad. Sci. USA, 2004, vol. 101, pp. 10205-10210.
17. Tolstikov, V.V., Lommen, A., Nakanishi, K., Tanaka, N., and Fiehn, O., Anal. Chem., 2003, vol. 75, pp. 6737-6740.
18. De Vos, R.C., Moco, S., Lommen, A., Keurentjes, J.J., Bino, R.J., and Hall, R.D., Nature Protocols, 2007, vol. 2, pp. 778-791.
19. Wilson, I.D., Nicholson, J.K., Castro-Perez, J., Granger, J.H., Johnson, K.A., Smith, B.W., and Plumb, R.S., J. Proteome Res., 2005, vol. 4, pp. 591-598.
20. Wilson, I.D., Plumb, R., Granger, J., Major, H., Williams, R, and Lenz, E.M., J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 2005, vol. 817, pp. 67-76.
21. Roy, S.M. and Becker, C.H., Methods Mol. Biol., 2007, vol. 359, pp. 87-105.
22. Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T.A., Hill, L.R., Norton, S., Kumar, P., Anderle, M., and Becker, C.H., Anal. Chem., 2003, vol. 75, pp. 4818-4826.
23. Tolstikov, V.V. and Fiehn, O., Anal. Biochem., 2002, vol. 301, pp. 298-307.
24. Tolstikov, V.V., Fiehn, O., and Tanaka, N., Methods Mol. Biol., 2007, vol. 358, pp. 141-155.
25. Naidong, W., J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 2003, vol. 796, pp. 209-224.
26. Lafaye, A., Junot, C., Ramounet-Le Gall, B., Fritsch, P., Tabet, J.C., and Ezan, E., Rapid Commun. Mass Spectrom., 2003, vol. 17, pp. 2541-2549.
27. Idborg-Bjorkman, H., Edlund, P.O., Kvalheim, O.M., Schuppe-Koistinen, I., and Jacobsson, S.P., Anal. Chem., 2003, vol. 75, pp. 4784-4792.
28. Plumb, R., Granger, J., Stumpf, C., Wilson, I.D., Evans, J.A., and Lenz, E.M., Analyst., 2003, vol. 128, pp. 819-823.
29. Plumb, R.S., Stumpf, C.L., Granger, J.H., Castro-Perez, J., Haselden, J.N., and Dear, G.J., Rapid Commun. Mass Spectrom., 2003, vol. 17, pp. 2632-2638.
30. Williams, R.E., Major, H., Lock, E.A., Lenz, E.M., and Wilson, I.D., Toxicology, 2005, vol. 207, pp. 179-190.
31. Lenz, E.M., Bright, J., Knight, R., Wilson, I.D., and Major, H., Analyst., 2004, vol. 129, pp. 535-541.
32. Lenz, E.M., Bright, J., Knight, R., Wilson, I.D., and Major, H., J. Pharm. Biomed. Anal., 2004, vol. 35, pp. 599-608.
33. Nielsen, K.F. and Smedsgaard, J., J. Chromatogr. A, 2003, vol. 1002, pp. 111-136.
34. Colebatch, G., Desbrosses, G., Ott, T., Krusell, L., Montanari, O., Kloska, S., Kopka, J., and Udvardi, M.K., Plant J., 2004, vol. 39, pp. 487-512.
35. Jonsson, P., Gullberg, J., Nordstrom, A., Kusano, M., Kowalczyk, M., Sjostrom, M., and Moritz, T., Anal. Chem., 2004, vol. 76, pp. 1738-1745.
36. Roessner, U., Wagner, C., Kopka, J., Trethewey, R.N., and Willmitzer, L., Plant J., 2000, vol. 23, pp. 131-142.
37. Fu, X., Iga, M., Kimura, M., and Yamaguchi, S., Early Hum. Dev., 2000, vol. 58, pp. 41-55.
38. Roessner, U., Luedemann, A., Brust, D., Fiehn, O., Linke, T., Willmitzer, L., and Fernie, A., Plant Cell, 2001, vol. 13, pp. 11-29.
39. Roessner, U., Willmitzer, L., and Fernie, A.R., Plant Physiol., 2001, vol. 127, pp. 749-764.
40. Winder, C.L., Dunn, W.B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G.M., and Goodacre, R., Anal. Chem., 2008, vol. 80, pp. 2939-2948.
41. O'Hagan, S., Dunn, W.B., Brown, M., Knowles, J.D., and Kell, D.B., Anal. Chem., 2005, vol. 77, pp. 290-303.
42. Jiye, A., Trygg, J., Gullberg, J., Johansson, A.I., Jonsson, P., Antti, H., Marklund, S.L., and Moritz, T., Anal. Chem., 2005, vol. 77, pp. 8086-8094.
43. Watson, N.E., Vanwingerden, M.M., Pierce, K.M., Wright, B.W., and Synovec, R.E., J. Chromatogr, A., 2006, vol. 1129, pp. 111-118.
44. Dalluge, J., Beens, J., and Brinkman, U.A.T., J. Chromatogr. A, 2003, vol. 1000, pp. 69-108.
45. Welthagen, W. and Shellie, R.A., Metabolomics, 2005, vol. 1, pp. 65-73.
46. Adahchour, M., Brandt, M., Baier, H.U., Vreuls, R.J., Batenburg, A.M., and Brinkman, U.A., J. Chromatogr. A, 2005, vol. 1067, pp. 245-254.
47. Guo, X. and Lidstrom, M.E., Biotechnol. Bioeng., 2008, vol. 99, pp. 929-940.
48. Monton, M.R. and Soga, T., J. Chromatogr. A, 2007, vol. 1168(1-2), pp. 237-246.
49. Klampfl, C.W., J. Chromatogr. A, 2004, vol. 1044, pp. 131-144.
50. Kuhara, T., Mass Spectrom. Rev., 2005, vol. 24, pp. 814-827.
51. Piraud, M., Vianey-Saban, C., Petritis, K., Elfakir, C., Steghens, J.P., Morla, A., and Bouchu, D., Rapid Commun. Mass Spectrom., 2003, vol. 17, pp. 1297-1311.
52. Schulze, A., Lindner, M., Kohlmuller, D., Olgemoller, K., Mayatepek, E., and Hoffmann, G.F., Pediatrics, 2003, vol. 111, pp. 1399-1406.
53. Chace, D.H., Kalas, T.A., and Naylor, E.W., Clin. Chem., 2003, vol. 49, pp. 1797-1817.
54. Chace, D.H., Kalas, T.A., and Naylor, E.W., Annu. Rev. Genomics Hum. Genet., 2002, vol. 3, pp. 17-45.
55. Chace, D.H. and Kalas, T.A., Clin. Biochem., 2005, vol. 38, pp. 296-309.
56. Watkins, S.M., Reifsnyder, P.R., Pan, H.J., German, J.B., and Leiter, E.H., J. Lipid Res., 2002, vol. 43, pp. 1809-1817.
57. German, J.B., Roberts, M.A., and Watkins, S.M., J. Nutr., 2003, vol. 133, pp. 2078-2083.
58. Snyder, A.P., McClennen, W.H., Dworzanski, J.P., and Meuzelaar, H.L., Anal. Chem., 1990, vol. 62, pp. 2565-2573.
59. Hermansson, M., Uphoff, A., Kakela, R., and Somerharju, P., Anal. Chem., 2005, vol. 77, pp. 2166-2175.
60. Han, X. and Gross, R.W., J. Lipid Res., 2003, vol. 44, pp. 1071-1079.
61. Han, X. and Gross, R.W., Mass Spectrom. Rev., 2005, vol. 24, pp. 367-412.
62. Hsu, F.F. and Turk, J., J. Am. Soc. Mass Spectrom., 1999, vol. 10, pp. 587-599.
63. Duffin, K.L., Henion, J.D., and Shieh, J.J., Anal. Chem., 1991, vol. 63, pp. 1781-1788.
64. Pulfer, M. and Murphy, R.C., Mass Spectrom. Rev., 2003, vol. 22, pp. 332-364.
65. Griffiths, W.J., Jonsson, A.P., Liu, S., Rai, D.K., and Wang, Y., Biochem J., 2001, vol. 355, pp. 545-561.
66. Jonsson, P., Bruce, S.J., Moritz, T., Trygg, J., Sjostrom, M., Plumb, R., Granger, J., Maibaum, E., Nicholson, J.K., Holmes, E., and Antti, H., Analyst., 2005, vol. 130, pp. 701-707.
67. Smilde, A.K., Jansen, J.J., Hoefsloot, H.C., Lamers, R.J., van der Greef, J., and Timmerman, M.E., Bioinformatics, 2005, vol. 21, pp. 3043-3048.
68. Chang, W.T., Thissen, U., Ehlert, K.A., Koek, M.M., Jellema, R.H., Hankemeier, T., van der Greef, J., and Wang, M., Planta Med., 2006, vol. 72, pp. 458-467.
69. Vis, D.J., Westerhuis, J.A., Smilde, A.K., and van der Greef, J., BMC Bioinformatics, 2007, vol. 8, p. 322.
70. Broeckling, C.D., Reddy, I.R., Duran, A.L., Zhao, X., and Sumner, L.W., Anal. Chem., 2006, vol. 78, pp. 4334-4341.
71. 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., FEBS Lett., 2005, vol. 579, pp. 1332-1337.
72. Stein, S.E., J. Am. Soc. Mass Spectrom., 1999, vol. 10, pp. 770-781.
73. Jansen, R., Lachatre, G., and Marquet, P., Clin. Biochem., 2005, vol. 38, pp. 362-372.
74. Bristow, A.W., Webb, K.S., Lubben, A.T., and Halket, J., Rapid Commun. Mass Spectrom., 2004, vol. 18, pp. 1447-1454.
75. Lemire, S.W. and Busch, K.L., J. Mass Spectrom., 1996, vol. 31, pp. 280-288.
76. Josephs, J.L. and Sanders, M., Rapid Commun. Mass Spectrom., 2004, vol. 18, pp. 743-759.
77. 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., Ther. Drug Monit., 2005, vol. 27, pp. 747-751.
78. Pelander, A., Ojanpera, I., Laks, S., Rasanen, I., and Vuori, E., Anal. Chem., 2003, vol. 75, pp. 5710-5718.
79. Halket, J.M., Waterman, D., Przyborowska, A.M., Patel, R.K., Fraser, P.D., and Bramley, P.M., J. Exp. Bot., 2005, vol. 56, pp. 219-243.