Optimizing the use of quality control samples for signal drift correction in large-scale urine metabolic profiling studies

Analytical Chemistry

Volumn 84, Issue 6, 2012, Pages 2670-2677

  Kamleh, Muhammad Anas ^a,b   Ebbels, Timothy M D ^a   Spagou, Konstantina ^a,c   Masson, Perrine ^a   Want, Elizabeth J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b DAMASCUS UNIVERSITY   (Syrian Arab Republic)

^c ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS TIME; ANALYTICAL METHOD; BIO-MARKER DISCOVERY; COEFFICIENT OF VARIATION; FEATURE-BASED; HYPOTHESIS GENERATION; METABOLIC PROFILING; PHENOTYPING; REPRODUCIBILITIES; SAMPLE INJECTION; SEQUENCE DESIGNS; SIGNAL CORRECTION; SIGNAL DRIFT; URINE SAMPLE;

BODY FLUIDS; METABOLITES; OPTIMIZATION; QUALITY CONTROL; TRACE ANALYSIS;

METABOLISM;

ANIMAL; ARTICLE; CHEMISTRY; ELECTROSPRAY MASS SPECTROMETRY; EVALUATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; METABOLOME; METABOLOMICS; METHODOLOGY; QUALITY CONTROL; RAT; REPRODUCIBILITY; URINALYSIS; URINE;

ANIMALS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; METABOLOME; METABOLOMICS; QUALITY CONTROL; RATS; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; URINALYSIS; URINE;

EID: 84858710198     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac202733q     Document Type: Article

References (37)

1. Nicholson, J. K.; Lindon, J. C. Nature 2008, 455, 1054-1056
2. Kell, D. B. Drug Discovery Today 2006, 11, 1085-1092
3. Wishart, D. S.; Knox, C.; Guo, A. C.; Eisner, R.; Young, N.; Gautam, B.; Hau, D. D.; Psychogios, N.; Dong, E.; Bouatra, S.; Mandal, R.; Sinelnikov, I.; Xia, J.; Jia, L.; Cruz, J. A.; Lim, E.; Sobsey, C. A.; Shrivastava, S.; Huang, P.; Liu, P.; Fang, L.; Peng, J.; Fradette, R.; Cheng, D.; Tzur, D.; Clements, M.; Lewis, A.; De Souza, A.; Zuniga, A.; Dawe, M.; Xiong, Y.; Clive, D.; Greiner, R.; Nazyrova, A.; Shaykhutdinov, R.; Li, L.; Vogel, H. J.; Forsythe, I. Nucleic Acids Res. 2009, 37, D603-610
4. Dai, H.; Xiao, C.; Liu, H.; Hao, F.; Tang, H. J. Proteome Res. 2010, 9, 1565-1578
5. Geier, F. M.; Want, E.; Leroi, A. M.; Bundy, J. G. Anal. Chem. 2011, 83, 3730-3736
6. Lindon, J. C.; Holmes, E.; Bollard, M. E.; Stanley, E. G.; Nicholson, J. K. Biomarkers 2004, 9, 1-31
7. Yap, I. K. S.; Brown, I. J.; Chan, Q.; Wijeyesekera, A.; Garcia-Perez, I.; Bictash, M.; Loo, R. L.; Chadeau-Hyam, M.; Ebbels, T.; Iorio, M. D.; Maibaum, E.; Zhao, L.; Kesteloot, H.; Daviglus, M. L.; Stamler, J.; Nicholson, J. K.; Elliott, P.; Holmes, E. J. Proteome Res. 2010, 9, 6647-6654
8. Bictash, M.; Ebbels, T. M.; Chan, Q.; Loo, R. L.; Yap, I. K. S.; Brown, I. J.; de Iorio, M.; Daviglus, M. L.; Holmes, E.; Stamler, J.; Nicholson, J. K.; Elliott, P. J. Clin. Epidemiol. 2010, 63, 970-979
9. Patterson, S. D.; Cohen, N.; Karnoub, M.; Truter, S. L.; Emison, E.; Khambata-Ford, S.; Spear, B.; Ibia, E.; Sproule, R.; Barnes, D.; Bhathena, A.; Bristow, M. R.; Russell, C.; Wang, D.; Warner, A.; Westelinck, A.; Brian, W.; Snapir, A.; Franc, M. A.; Wong, P.; Shaw, P. M. Pharmacogenomics 2011, 12, 939-951
10. Keun, H. C.; Ebbels, T. M. D.; Antti, H.; Bollard, M. E.; Beckonert, O.; Schlotterbeck, G.; Senn, H.; Niederhauser, U.; Holmes, E.; Lindon, J. C.; Nicholson, J. K. Chem. Res. Toxicol. 2002, 15, 1380-1386
11. Dumas, M.-E.; Maibaum, E. C.; Teague, C.; Ueshima, H.; Zhou, B.; Lindon, J. C.; Nicholson, J. K.; Stamler, J.; Elliott, P.; Chan, Q.; Holmes, E. Anal. Chem. 2006, 78, 2199-2208
12. Begley, P.; Francis-McIntyre, S.; Dunn, W. B.; Broadhurst, D. I.; Halsall, A.; Tseng, A.; Knowles, J.; Goodacre, R.; Kell, D. B. Anal. Chem. 2009, 81, 7038-7046
13. Zelena, E.; Dunn, W. B.; Broadhurst, D.; Francis-McIntyre, S.; Carroll, K. M.; Begley, P.; O'Hagan, S.; Knowles, J. D.; Halsall, A.; Wilson, I. D.; Kell, D. B. Anal. Chem. 2009, 81, 1357-1364
14. Draisma, H. H. M.; Reijmers, T. H.; van der Kloet, F.; Bobeldijk-Pastorova, I.; Spies-Faber, E.; Vogels, J. T. W. E.; Meulman, J. J.; Boomsma, D. I.; van der Greef, J.; Hankemeier, T. Anal. Chem. 2010, 82, 1039-1046
15. van der Kloet, F. M.; Bobeldijk, I.; Verheij, E. R.; Jellema, R. H. J. Proteome Res. 2009, 8, 5132-5141
16. Bijlsma, S.; Bobeldijk, I.; Verheij, E. R.; Ramaker, R.; Kochhar, S.; Macdonald, I. A.; van Ommen, B.; Smilde, A. K. Anal. Chem. 2005, 78, 567-574
17. Giavalisco, P.; Kohl, K.; Hummel, J.; Seiwert, B.; Willmitzer, L. Anal. Chem. 2009, 81, 6546-6551
18. Roy, S. M.; Becker, C. H. Quant. Proteomics Mass Spectrom. 2007, 87-105
19. Sysi-Aho, M.; Katajamaa, M.; Yetukuri, L.; Oresic, M. BMC Bioinf. 2007, 8, 93
20. Gika, H. G.; Macpherson, E.; Theodoridis, G. A.; Wilson, I. D. J. Chromatogr., B 2008, 871, 299-305
21. Lai, L.; Michopoulos, F.; Gika, H.; Theodoridis, G.; Wilkinson, R. W.; Odedra, R.; Wingate, J.; Bonner, R.; Tate, S.; Wilson, I. D. Mol. Biosyst. 2010, 6, 108-120
22. Kamleh, M. A.; Dow, J. A. T.; Watson, D. G. Briefings Funct. Genomics Proteomics 2009, 8, 28-48
23. Guy, P. A.; Tavazzi, I.; Bruce, S. J.; Ramadan, Z.; Kochhar, S. J. Chromatogr., B 2008, 871, 253-260
24. Dunn, W. B.; Broadhurst, D.; Begley, P.; Zelena, E.; Francis-McIntyre, S.; Anderson, N.; Brown, M.; Knowles, J. D.; Halsall, A.; Haselden, J. N.; Nicholls, A. W.; Wilson, I. D.; Kell, D. B.; Goodacre, R. Nat. Protoc. 2011, 6, 1060-1083
25. Coen, M.; Hong, Y. S.; Clayton, T. A.; Rohde, C. M.; Pearce, J. T.; Reily, M. D.; Robertson, D. G.; Holmes, E.; Lindon, J. C.; Nicholson, J. K. J. Proteome Res. 2007, 6, 2711-2719
26. Want, E. J.; Wilson, I. D.; Gika, H.; Theodoridis, G.; Plumb, R. S.; Shockcor, J.; Holmes, E.; Nicholson, J. K. Nat. Protoc. 2010, 5, 1005-1018
27. Chiogna, M.; Massa, M. S.; Risso, D.; Romualdi, C. BMC Bioinf. 2009, 10, 61
28. Cuadros-Inostroza, A.; Giavalisco, P.; Hummel, J.; Eckardt, A.; Willmitzer, L.; Peña-Cortés, H. Anal. Chem. 2010, 82, 3573-3580
29. Craig, A.; Cloarec, O.; Holmes, E.; Nicholson, J. K.; Lindon, J. C. Anal. Chem. 2006, 78, 2262-2267
30. t'Kindt, R.; Scheltema, R. A.; Jankevics, A.; Brunker, K.; Rijal, S.; Dujardin, J.-C.; Breitling, R.; Watson, D. G.; Coombs, G. H.; Decuypere, S. PLoS Negl. Trop. Dis. 2011, 4, e904
31. Jouan-Rimbaud, D.; Massart, D. L.; Saby, C. A.; Puel, C. Chemom. Intell. Lab. Syst. 1998, 40, 129-144
32. Masson, P.; Alves, A. C.; Ebbels, T. M. D.; Nicholson, J. K.; Want, E. J. Anal. Chem. 2010, 82, 7779-7786
33. Centre for Drug Evaluation and Research (CDER). FDA Guidance for Industry, Bioanalytical Method Validation, May 2001.
34. Smith, C. A.; Want, E. J.; O'Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779-787
35. Richard, A. S.; Anas, K.; David, W.; Charles, E.; David, G. W.; Michael, P. B.; Ritsert, C. J.; Rainer, B. Proteomics 2008, 8, 4647-4656
36. Kamleh, M. A.; Hobani, Y.; Dow, J. A. T.; Watson, D. G. FEBS Lett. 2008, 582, 2916-2922
37. Kaddurah-Daouk, R.; Baillie, R.; Zhu, H.; Zeng, Z.-B.; Wiest, M.; Nguyen, U.; Watkins, S.; Krauss, R. Metabolomics 2010, 6, 191-201