Challenges in mass spectrometry based targeted metabolomics

Current Molecular Medicine

Volumn 10, Issue 2, 2010, Pages 216-226

  Koal, T ^a   Deigner, H P ^a  

^a BIOCRATES LIFE SCIENCES AG   (Austria)

Author keywords

Biomarker; Mass spectrometry; Matrix effects; Metabolomics; Reference material; Stability; Standardization; Targeted metabolomics

Indexed keywords

BIOLOGICAL MARKER;

ACCURACY; CARBON NUCLEAR MAGNETIC RESONANCE; DRUG MONITORING; ENDOSCOPIC MUCOSAL RESECTION; FLOW INJECTION ANALYSIS; GAS CHROMATOGRAPHY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; NITROGEN NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; STANDARDIZATION; VALIDATION STUDY;

ANIMALS; BIOLOGICAL MARKERS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENOMICS; HUMANS; MASS SPECTROMETRY; METABOLOME; METABOLOMICS; MICE; MODELS, BIOLOGICAL; TIME FACTORS;

EID: 77951031841     PISSN: 15665240     EISSN: None     Source Type: Journal    
DOI: 10.2174/156652410790963312     Document Type: Review

References (136)

1. Blow, N. (2008) Nature, 455, 697-700.
2. Curtin, C. (2008) Genome Technol., 31-35.
3. Horgan, R.P., Clany, O.H., Myers, J.E. and Baker, P.N. (2009) BJOG, 116, 173-181.
4. Ryan, D. and Robards, K. (2006) Anal Chem., 78, 7954-7958.
5. Nicholson, J.K. and Lindon, J.C. (2008) Nature, 455, 1054-1056.
6. Lindon, J.C., Holmes, E. and Nicholson, J.K. FEBS (2007) Journal, 274, 1140-1151.
7. Spratlin, J.L., Serkova, N.J. and Eckhardt, S.G. (2009) Clin. Cancer Res., 15, 431-440.
8. Kell, D.B. (2004) Curr. Opinion. Microbiol., 7, 296-307.
9. Fiehn, O. (2002) Plant Molecul. Biolog., 48, 155-171.
10. Hollywood, K., Brison, D.R. and Goodacre, R. (2006) Proteomics, 6, 4716-4723.
11. Want, E.J., Nordström, A., Morita, H. and Siuzdak, G. (2007) J. Proteome. Res., 6, 459-468.
12. Lu, W., Bennett, B.D. and Rabinowitz, J.D. (2008) J. Chromatogr. B, 871, 236-242.
13. Dunn, W.B., Bailey, N.J.C. and Johnson, H.E. (2005) Analyst, 130, 606-625.
14. Feng, X., Liu, X., Luo, Q. and Liu, B.F. (2008) Mass Spectrom. Rev., 27, 635-660.
15. Dettmer, K. Aronov, P.A. and Hammock, B.D. (2007) Mass Spectrom. Rev., 26, 51-78.
16. Nielsen, J. and Oliver, S. (2005) Trends Biotechnol., 23, 544-546.
17. Werner, E., Heilier, J.F., Ducruix, C., Ezan, E. and Junot, C. (2008) J. Chromatogr. B, 871, 143-163.
18. Van, Q.N., Veenstra, T.D. (2009) Genome Medicine, 1, 5.
19. Issaq, H.J., Que, N. Van, Waybright, T.J., Muschik, G.M. and Veenstra, T.D. (2009) J. Sep. Sci., 32, 2183-2199.
20. Griffiths, W.J. and Wang, Y. (2009) Chem. Soc. Rev., 38, 1882-1896.
21. Hu, C., van der Heijden, R., Wang, M., van der Greef, J., Hankemeier, T. and Xu, G. (2009) J. Chromatogr. B, 877,2836-2846.
22. Lowe, R.G., Lord, M., Rybak, K., Trengove, R.D., Oliver, R.P. and Solomon P.S. (2009) Fungal Genet. Biol., 46, 381-389.
23. Sawada, Y., Akiyama, K., Sakata, A., Kuwahara, A., Otsuki, H., Sakurai, T., Saito, K. and Hirai, M. Y. (2009) Plant Cell. Physiol., 50, 37-47.
24. Lowe, R.G., Lord, M., Rybak, K., Trengove, R.D., Oliver, R.P. and Solomon, P.S. (2008) Fungal Genet. Biol., 45, 1479-1486.
25. Hanhineva, K., Rogachev, I., Kokko, H., Mintz-Oron, S., Venger, I., Karenlampi, S. and Aharoni, A. (2008) Phytochemistry, 69, 2463-2481.
26. Rochfort, S.J., Trenerry, V.C., Imsic, M., Panozzo, J. and Jones, R. (2008) Phytochemistry, 69, 1671-1679.
27. Altmaier, E., Ramsay, S.L., Graber, A., Mewes, H.W., Weinberger, K.M. and Suhre, K. (2008) Endocrinol., 149, 3478-3489.
28. Jackson, A.U., Werner, S.R., Talaty, N., Song, Y., Campbell, K., Cooks, R.G. and Morgan, J.A. (2008) Anal Biochem., 375, 272-281.
29. Koves, T.R., Ussher, J.R., Noland, R.C., Slentz, D., Mosedale, M., Ilkayeva, O., Bain, J., Stevens, R., Dyck, J.R., Newgard, C.B., Lopaschuk, G.D. and Muoio, D.M. (2008) Cell. Metab., 7, 45-56.
30. Griffiths, W.J., Karu, K., Hornshaw, M., Woffendin, G. and Wang, Y. (2007) Eur. J. Mass. Spectrom., 13, 45-50.
31. Wheelock, C.E., Goto, S., Hammock B.D. and Newman J.W. (2007) Metabolomics., 3, 137-145.
32. McNally, D.J., Aubry, A.J., Hui, J.P., Khieu, N.H., Whitfield, D., Ewing C.P., Guerry, P., Brisson, J.R., Logan. S.M. and Soo E.C. (2007) J. Biol. Chem., 282, 14463-14475.
33. Devaiah, S.P., Roth, M.R., Baughman, E., Li, M., Tamura, P., Jeannotte, R., Welti, R. and Wang, X. (2006) Phytochemistry, 67, 1907-1924.
34. Verdonk, J.C., de Ric, V., Verhoeven, H.A., Haring, M.A., van Tunen, A.J. and Schuurink, R.C. (2003) Phytochemistry, 62, 997-1008.
35. Ceglarek, U., Leichtler, A., Brügel, M., Kortz, L., Brauer, R., Bresler, K., Thiery, J. and Fiedler, G.M. (2008) Mol. Cell. Endocrinol., 301, 266-271.
36. Nordström, A. and Lewensohn, R. (2009) J. Neuroimmune. Pharmacol., [Epub ahead of print].
37. Vogeser, M. and Seger, C. (2008) Clin. Biochem., 41, 649-662.
38. Koal, T., Sibum, M., Koster, E., Resch, K. and Kaever, V. (2006) Clin. Chem. Lab. Med., 44, 299-305.
39. Koal, T., Burhenne, H., Römling, R., Svoboda, M., Resch, K. and Kaever, V. (2005) Rapid Commun. Mass. Spectrom., 19, 2995-3001.
40. Back, D., Gibbons, S. and Khoo, S. (2006) Ther. Drug Monit., 28, 468-473.
41. Poirier, J.M., Robidou, P. and Jaillon, P. (2005) Ther. Drug Monit., 27, 186-192.
42. Streit, F., Armstrong, V.W. and Oellerich, M. (2002) Clin. Chem., 48, 955-958.
43. Koal, T., Deters, M., Casetta, B. and Kaever, V. (2004) J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci., 805, 215-222.
44. Ceglarek, U. Lembcke, J., Fiedler, G.M., Werner, M., Witzigmann, H., Hauss, J.P. and Thiery, J. (2004) Clin. Chim. Acta, 346, 181-190.
45. Taylor, P.J. (2004) Ther. Drug Monit., 26, 215-219.
46. Saint-Marcoux, F., Sauvage, F.L. and Marquet, P. (2007) Anal. Bioanal. Chem., 388, 1327-1349.
47. van der Kooy, F., Maltese, F., Choi, Y.H., Kim, H.K. and Verpoorte, R. (2009) Planta Med., 75, 763-775.
48. Moco, S., Schneider, B. and Verfoort, J. (2009) J. Proteome Res., 8, 1694-1703.
49. Viant, M.R. (2008) Mol. BioSyst., 4, 980-986.
50. Oldiges, M., Lütz, S., Pflug, S., Schroer, K., Stein, N. and Wiendahl, C. (2007) Appl. Microbiol. Biotechnol., 76, 495-511.
51. Khoo, S.H. and Al-Rubeai, M. (2007) Biotechnol. Appl. Biochem., 47, 71-84.
52. Schaub, J. and Reuss, M. (2008) Biotechnol. Prog., 24, 1402-1407.
53. de la Luz-Hernández, K.R., Rojas-del Calvo, L., Rabasa-Legón, Y., Lage-Castellanos, A., Castillo-Vitlloch, A., Díaz, J. and Gaskell, S. (2008) J. Proteomics, 71, 133-147.
54. Heazell, A.E., Brown, M., Dunn, W.B., Worton, S.A., Crocker, I.P., Baker, P.N. and Kell, D.B. (2008) Placenta, 29, 691-698.
55. Cezar, G.G., Quam, J.A., Smith, A.M., Rosa, G.J., Piekarczyk, M.S., Brown, J.F., Gage, F.H. and Muotri, A.R. (2007) Stem Cells Dev., 16, 869-882.
56. Williams B.J., Cameron C.J., Workman R., Broeckling C.D., Sumner L.W. and Smith J.T. (2007) Electrophoresis, 28, 1371-1379.
57. Buchholz, A., Hurlebaus, J., Wandrey, C. and Takors, R. (2002) Biomol. Eng., 19, 5-15.
58. Ewald, J.C., Heux, S. and Zamboni N. (2009) Anal. Chem., 81, 3623-3629.
59. Brennan, L. (2008) Proc. Nutr. Soc., 67, 404-408.
60. Whitfield, P., German A.J. and Noble P.-J.M. (2004) Br. J. Nutr., 92, 549-555.
61. Clarke, C.J. and Haselden, J.N. (2008) Toxicol. Pathol., 36, 140-147.
62. German, J.B., Gillies, L.A., Smilowitz, J.T., Zivkovic, A.M. and Watkins, S.M. (2007) Curr. Opin. Lipidol., 18, 66-71.
63. Hunt A.N. (2006) Biochim. Biophysic. Acta, 1761, 577-587.
64. He, H., Conrad, C.A., Nilsson, C.L., Ji, Y., Schaub, T.M., Marshall, A.G. and Emmett, M.R. (2007) Anal. Chem., 79, 8423-8430.
65. Koulman, A., Woffendin, G., Narayana, V.K., Welchman, H., Crone, C. and Volmer, D.A. (2009) Rapid Commun. Mass Spectrom., 23, 1411-1418.
66. Pang L.-Q., Liang Q.-L., Wang Y.-M., Ping L. and Luo G.-A. (2008) J. Chromatogr. B., 869, 118-125.
67. Zehethofer N. and Pinto D.M. (2008) Anal. Chim. Acta, 627, 62-70.
68. Matyash, V., Liebisch G., Kurzchalia T.V., Shevchenko A. and Schwudke D. (2008) J. Lipid. Res., 49, 1137-1146.
69. Schwudke, D., Oegema J., Burton L., Entchev E., Hannich T., Ejsing C.S., Kurzchalia T. and Shevchenko A. (2006) Anal. Chem., 78, 585-595.
70. Murphy R.C., James P.F., McAnoy A.M., Krank J., Duchoslav E. and Barkley R.M. (2007) Anal. Biochem., 366, 59-70.
71. Zemski Berry K.A. and Murphy R.C. (2006) Anal. Biochem., 349, 118-128.
72. Willmann J., Leibfritz D. and Thiele H. (2008) J. Biomol. Tech., 19, 211-216.
73. Ogiso H., Suzuki T. and Taguchi R. (2008) Anal Biochem., 375, 124-131.
74. Liebisch G., Lieser B., Rathenberg J., Drobnik W. and Schmitz G. (2004) Biochim. Biophys. Acta, 1686, 108-117.
75. Han, X. and Jiang. X. (2009) Eur. J. Lipid. Sci. Technol., 111, 39-52.
76. Ejsing, C,S,, Sampaio, J.. Surendranath, V., Duchoslav, E., Ekroos, K., Klemm R.W., Simons. K. and Shevchenko. A. (2009) Proc. Natl. Acad. Sci. USA, 106, 2136-2141
77. Gross, R.W. and Han, X. (2009) Am. J. Physiol. Endocrinol. Metab., 297, E297-303.
78. Schwudke, D., Liebisch, G., Herzog, R., Schmitz, G. and Shevchenko, A. (2007) Methods Enzymol., 433, 175-191.
79. Wishart, D.S., Lewis, M.J., Morrissey, J.A., Flegel, M.D. Jeronic, K., Xiong, Y., Cheng, D., Eisner, R., Gautam, B., Tzur, D., Sawhney, S., Bamforth, F., Greiner, R. and Li, L. (2008) J. Chromatogr. B, 871, 164-173.
80. Griffin, J.L. (2006) Phil. Trans. R. Soc. B, 361, 147-161.
81. Gieger, C., Geistlinger, L., Altmaier, E., Hrabé de Angelis, M., Kronenberg, F., Meitinger, T., Mewes, H.-W. Wichmann, H.-E. Weinberger, K.M., Adamski, J., Illig, T. and Suhre, K. (2008) PLoS Genet., 4, 11.
82. Kiefer, P., Portais, J.-C. and Vorholt, J.A. (2008) Analyt. Biochem., 382, 94-100.
83. Zhang, N.R., Yu, S., Tiller, P., Yeh, S., Mahan, E. and Emary, W.B. (2009) Rapid Commun. Mass Spectrom., 23, 1085-1094.
84. Yanes, O., Woo, H.K., Northen, T.R., Oppenheimer, S.R., Shriver, L., Apon, J., Estrada, M.N., Potchoiba, M.J., Steenwyk, R., Manchester, M. and Siuzdak, G. (2009) Anal Chem., 81, 2969-2975.
85. Duarte, I.F., Legido-Quigley, C., Parker, D.A., Swann, J.R., Spraul, M., Braumann, U., Gil, A.M., Holmes, E., Nicholson, J.K., Murphy, G.M., Vilca-Melendez, H., Heaton, N. and Lindon, (2009) Mol. Biosyst., 5, 180-190.
86. Shulaev V. (2006) Brief Bioinform., 7, 128-139.
87. Ståhlmana, M., Ejsing, C.S., Tarasovc, K., Permana, J., Boréna, J., Ekroos, K. (2009) J. Chromatogr. B, 26, 2664-2672.
88. Han, X. (2007) Curr. Opin. Mol. Ther., 9, 586-591.
89. Yang, K., Cheng, H., Gross, R.W. and Han, X. (2009) Anal Chem., 81, 4356-4368.
90. Alpert, A.J., (1990) J. Chromatogr. A, 499, 177-196.
91. Cubbon, S., Antonio, C., Wilson, J. and Thomas-Oates, (2009) J. Mass Spectrom. Rev., [Epub ahead of print].
92. T'kindt, R., Storme, M., Deforce, D. and Van Bocxlaer J. (2008) J. Sep. Sci., 31, 1609-1614.
93. Tolstikov, V.V. (2009) Methods Mol. Biol., 544, 343-353.
94. Plumb, R.S., Rainville, P.D., Potts, W.B.3rd, Johnson, K.A., Gika, E., Wilson, I.D. (2009) J. Proteome Res., 8, 2495-2500.
95. Flores-Valverde, A.M. and Hill, E.M. (2008) Anal. Chem., 80, 8771-8779.
96. Wang, X., Lv, H., Sun, H., Liu, L., Yang, B., Sun, W., Wang, P., Zhou, D., Zhao, L., Dou, S., Zhang, G. and Cao, H. (2008) J. Pharm. Biomed. Anal, 48, 1161-1168.
97. Kind, T., Tolstikov, V., Fiehn, O. and Weiss, R.H. (2007) Anal. Biochem., 363, 185-195.
98. Ramautar, R., Somsen, G.W., de Jong, G.J. (2009) Electrophoresis, 30, 276-291.
99. Lapainis T., Rubakhin S.S., Sweedler J.V. (2009) Anal. Chem., 81, 5858-5864.
100. Rauh M. (2008) Mol. Cell Endocrinol., 301, 272-281.
101. Kaddurah-Daouk, R. and Krishnan, K.R.R. (2009) Neuropsychopharmacology, 34, 173-186.
102. http://www.biocrates.com/images/stories/pdf/Targeted%20Metabolomics-A4. pdf (search 24.08.2009)
103. Sonntag, D. (2009) GIT Laboratory Journal, 12-13.
104. http://www.cstl.nist.gov/projects/fy06/health0683905.pdf (search 24.08.2009)
105. http://www.cstl.nist.gov/projects/fy06/health0683901.pdf (search 24.08.2009)
106. http://www.nist.gov/cstl/analytical/organic/metabolitesinserum.cfm (search 24.08.2009)
107. http://www.webconferences.com/nihsacghs/ppt/Phinney.ppt (search 24.08.2009)
108. Dodder N. G., Oral Presentation at ASMS 2009.
109. Guidance for Industry/Bioanalyical Method Validation, U.S. Department of Health and Human Services, Food and drug Administration, http://www.fda.gov/ downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM070107.pdf (search 24.09.2009)
110. Peters, F.T. (2007) Anal. Bioanal. Chem., 388, 1505-1519.
111. Unterwurzacher, I., Koal, T., Bonn, G.K., Weinberger, K.M., Ramsay, S.L. (2008) Clin. Chem. Lab. Med., 46,1589-1597.
112. Morrow, J.D. and Roberts, L.J. (1994) Methods Enzymol., 233, 163-174.
113. Dadgar, D., Burnett, P.E. (1995) J. Pharm. Biomed. Anal., 14, 23-31.
114. Human Metabolome Database, Available at: http://www.hmdb.ca (search 24.08.2009)
115. Metz, T.O., Page, J.S., Baker, E.S., Tang, K., Ding, J., Shen, Y. and Smith, R.D. (2008) Trends Analyt. Chem., 27, 205-214.
116. Beaudry, F. and Vachon, P. (2006) Biomed. Chromatogr., 20, 200-205.
117. Tang, K. and Smith, R.J. (2001) Am. Soc. Mass Spectrom., 12, 343-347.
118. Schmidt, A., Karas, M., Dülcks, T.J. (2003) Am. Soc. Mass Spetrom., 14, 492-500.
119. Tang, K., Page, J. and Smith, R.J. (2004) Am. Soc. Mass Spectrom., 15, 1416-1423.
120. Cech, N. and Enke, C. (2000) Anal. Chem., 72, 2717-2723.
121. van Eeckhaut, A., Lanckmans, K., Sarre, S., Smolders, I., Michotte, Y. (2009) J. Chromatogr. B, 877, 2198-2207.
122. Xu, R.N., Fan, L., Rieser, M.J. and El-Shourbagy, T.A. (2007) J. Pharmaceut. Biomed. Analysis, 44, 342-355.
123. Bakhtiar, R. and Majumda, T.K., (2007) J. Pharmacol. Toxicol. Methods, 55, 227-243.
124. Jemal, M. and Xia, Y.-Q. (2006) Curr. Drug Metab., 7, 491-502.
125. Samyn, N., Laloup, M. and De Boeck, G. (2007) Anal. Bioanal. Chem., 388, 1437-1453.
126. Liang, H.R., Foltz, R.L., Meng, M. and Bennett, P. (2003) Rapid Commun. Mass Spctrom., 17, 2815-2821.
127. Sojo, L.E., Lum, G. and Chee, P. (2003) Analyst, 128, 51-54.
128. Dolan, J.W. (2001) LC-GC Europe, 11, 664-667.
129. Koulman, A., Lane, G.A., Harrison, S.J. and Volmer, D.A. (2009) Anal. Bioanal. Chem., 394, 663-670.
130. Marrer, E. and Dieterle, F. (2008) Expert Opin. Drug Metab. Toxicol., 4, 1391-1402
131. Tohge, T. and Fernie, A.R. (2009) Phytochem., 70, 450-456.
132. Yetukuri, L., Katajamaa, M., Medina-Gomez, G., Seppänen-Laakso, T., Vidal-Puig, A. and Orešič, M. (2007) BMC Syst. Biol., 1, 12.
133. Marrer E., Dieterle, F. (2007) Chem. Biol. Drugs Des., 69, 381-394.
134. Kohl, M. (2009) Curr. Mol. Med. Submitted.
135. Sumner, L.W., Mendes, P. and Dixon, R.A. (2003) Phytochemistry, 62, 817-836.
136. 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., Wetserhoff, H.V., van Dam, K. and Oliver, S.G., (2001) Nat. Biotechnol., 19, 45-50.