Evaluation and optimization of metabolome sample preparation methods for Saccharomyces cerevisiae

Analytical Chemistry

Volumn 85, Issue 4, 2013, Pages 2169-2176

  Kim, Sooah ^a   Lee, Do Yup ^b   Wohlgemuth, Gert ^c   Park, Hyong Seok ^a   Fiehn, Oliver ^c   Kim, Kyoung Heon ^a  

^a Korea University   (South Korea)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE ANALYSIS; ACETONITRILE/WATER MIXTURES; CELL LEAKAGE; EXTRACELLULAR METABOLITES; EXTRACTION SOLVENTS; INTRACELLULAR METABOLITES; METABOLITE EXTRACTION; METABOLOMES; METABOLOMICS DATA; PURE METHANOLS; S.CEREVISIAE; SAMPLE PREPARATION; SAMPLE PREPARATION METHODS; SAMPLING PROTOCOL; SYSTEMATIC EVALUATION;

BIOMOLECULES; ENZYME ACTIVITY; ETHANOL; EXTRACTION; IMPORTANCE SAMPLING; MASS SPECTROMETRY; METABOLITES; METHANOL; QUENCHING; WATER FILTRATION; YEAST;

ORGANIC SOLVENTS;

ACETONITRILE; ACETONITRILE DERIVATIVE; ALCOHOL; METHANOL;

ARTICLE; CHEMISTRY; FILTRATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; METABOLISM; METABOLOME; PRINCIPAL COMPONENT ANALYSIS; SACCHAROMYCES CEREVISIAE;

ACETONITRILES; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; ETHANOL; FILTRATION; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; METABOLOME; METHANOL; PRINCIPAL COMPONENT ANALYSIS; SACCHAROMYCES CEREVISIAE;

EID: 84874088716     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac302881e     Document Type: Article

References (38)

1. Ha, S.-J.; Galazka, J. M.; Kim, S. R.; Choi, J.-H.; Yang, X.; Seo, J.-H.; Glass, N. L.; Cate, J. H. D.; Jin, Y.-S. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 504-509
2. Huo, Y.-X.; Cho, K. M.; Rivera, J. G. L.; Monte, E.; Shen, C. R.; Yan, Y.; Liao, J. C. Nat. Biotechnol. 2011, 29, 346-351
3. Stephanopoulos, G. Science 2007, 315, 801-804
4. Galazka, J. M.; Tian, C.; Beeson, W. T.; Martinez, B.; Glass, N. L.; Cate, J. H. D. Science 2010, 330, 84-86
5. Fiehn, O. Comp. Funct. Genom. 2001, 2, 155-168
6. Ryan, D.; Robards, K. Anal. Chem. 2006, 78, 7954-7958
7. van der Werf, M. J.; Jellema, R. H.; Hankemeier, T. J. Ind. Microbiol. Biotechnol. 2005, 32, 234-252
8. Hasunuma, T.; Sanda, T.; Yamada, R.; Yoshimura, K.; Ishii, J.; Kondo, A. Microb. Cell Fact. 2011, 10, 2
9. Fiehn, O. Plant Mol. Biol. 2002, 48, 155-171
10. de Koning, W.; van Dam, K. Anal. Biochem. 1992, 204, 118-123
11. Ding, M.-Z.; Zhuo, X.; Yuan, Y.-J. Metabolomics 2010, 6, 42-55
12. Gonzalez, B.; François, J.; Renaud, M. Yeast 1997, 13, 1347-1355
13. van Dam, J. C.; Eman, M. R.; Frank, J.; Lange, H. C.; van Dedem, G. W. K.; Heijnen, S. J. Anal. Chim. Acta 2002, 460, 209-218
14. Castrillo, J. I.; Hayes, A.; Mohammed, S.; Gaskell, S. J.; Oliver, S. G. Phytochemistry 2003, 62, 929-937
15. Villas-Boîas, S. G.; Højer-Pedersen, J.; Åkesson, M.; Smedsgaard, J.; Nielsen, J. Yeast 2005, 22, 1155-1169
16. Devantier, R.; Scheithauer, B.; Villas-Boîas, S. G.; Pedersen, S.; Olsson, L. Biotechnol. Bioeng. 2005, 90, 703-714
17. Wu, L.; Mashego, M. R.; van Dam, J. C.; Proell, A. M.; Vinke, J. L.; Ras, C.; van Winden, W. A.; van Gulik, W. M.; Heijnen, J. J. Anal. Biochem. 2005, 336, 164-171
18. Canelas, A. B.; Ras, C.; ten Pierick, A.; van Dam, J. C.; Heijnen, J. J.; van Gulik, W. M. Metabolomics 2008, 4, 226-239
19. Canelas, A. B.; ten Pierick, A.; Ras, C.; Seifar, R. M.; van Dam, J. C.; van Gulik, W. M.; Heijnen, J. J. Anal. Chem. 2009, 81, 7379-7389
20. Schneider, K.; Kromer, J. O.; Wittmann, C.; Alves-Rodrigues, I.; Meyerhans, A.; Diez, J.; Heinzle, E. Microb. Cell Fact. 2009, 8, 12
21. Boer, V. M.; Crutchfield, C. A.; Bradley, P. H.; Botstein, D.; Rabinowitz, J. D. Mol. Biol. Cell 2010, 21, 198-211
22. Shin, M. H.; Lee, D. Y.; Liu, K.-H.; Fiehn, O.; Kim, K. H. Anal. Chem. 2010, 82, 6660-6666
23. Wittmann, C.; Krömer, J. O.; Kiefer, P.; Binz, T.; Heinzle, E. Anal. Biochem. 2004, 327, 135-139
24. Link, H.; Anselment, B.; Weuster-Botz, D. Metabolomics 2008, 4, 240-247
25. Bolten, C. J.; Kiefer, P.; Letisse, F.; Portais, J.-C.; Wittmann, C. Anal. Chem. 2007, 79, 3843-3849
26. Villas-Boîas, S. G.; Roessner, U.; Hansen, M. A. E.; Smedsgaard, J.; Nielsen, J. Metabolome Analysis: An Introduction; John Wiley & Sons: Hoboken, NJ, 2007.
27. Mashego, M. R.; Jansen, M. L. A.; Vinke, J. L.; van Gulik, W. M.; Heijnen, J. J. FEMS Yeast Res. 2005, 5, 419-430
28. Ewald, J. C.; Heux, S.; Zamboni, N. Anal. Chem. 2009, 81, 3623-3629
29. Villas-Boîas, S. G.; Bruheim, P. Anal. Biochem. 2007, 370, 87-97
30. Theobald, U.; Mailinger, W.; Baltes, M.; Rizzi, M.; Reuss, M. Biotechnol. Bioeng. 1997, 55, 305-316
31. Lee, D. Y.; Fiehn, O. Plant Methods 2008, 4, 7
32. Fiehn, O.; Wohlgemuth, G.; Scholz, M.; Kind, T.; Lee, D. Y.; Lu, Y.; Moon, S.; Nikolau, B. Plant J. 2008, 53, 691-704
33. Denkert, C.; Budczies, J.; Weichert, W.; Wohlgemuth, G.; Scholz, M.; Kind, T.; Niesporek, S.; Noske, A.; Buckendahl, A.; Dietel, M.; Fiehn, O. Mol. Cancer 2008, 7, 72
34. Saeed, A. I.; Bhagabati, N. K.; Braisted, J. C.; Liang, W.; Sharov, V.; Howe, E. A.; Li, J.; Thiagarajan, M.; White, J. A.; Quackenbush, J. Methods Enzymol. 2006, 411, 134-193
35. Mo, M. L.; Palsson, B. Ø.; Herrgård, M. J. BMC Syst. Biol. 2009, 3, 37
36. Umetrics AB. In User's Guide to SIMCA-P, SIMCA-P+, ver. 11; Umetrics AB; Umea, Sweden, 2005.
37. Wang, R.; Fu, Y.; Lai, L. J. Chem. Inf. Comput. Sci. 1997, 37, 615-621
38. Zhang, T.; Fang, H. H. P. Biotechnol. Lett. 2004, 26, 989-992