Batch normalizer: A fast total abundance regression calibration method to simultaneously adjust batch and injection order effects in liquid chromatography/time-of-flight mass spectrometry-based metabolomics data and comparison with current calibration methods

Analytical Chemistry

Volumn 85, Issue 2, 2013, Pages 1037-1046

  Wang, San Yuan ^a   Kuo, Ching Hua ^a,b,c   Tseng, Yufeng J ^a,b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BATCH EFFECT; CALIBRATION METHOD; CHEMOMETRIC ANALYSIS; DATA SETS; FLIGHT MASS SPECTROMETRY; METABOLOMICS; METABOLOMICS DATA; NOVEL ALGORITHM; PEARSON CORRELATION COEFFICIENTS; PLASMA SAMPLES; REGRESSION CALIBRATION METHODS; REGRESSION MODEL; RELATIVE STANDARD DEVIATIONS; SYSTEMATIC BIAS;

ALGORITHMS; CHROMATOGRAPHIC ANALYSIS; CHROMATOGRAPHY; CORRELATION METHODS; LIQUIDS; MASS SPECTROMETRY; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS;

CALIBRATION;

ALGORITHM; ARTICLE; CALIBRATION; COMPARATIVE STUDY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; MASS SPECTROMETRY; METABOLOMICS; QUALITY CONTROL; STATISTICAL MODEL; TIME;

ALGORITHMS; CALIBRATION; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; HUMANS; LINEAR MODELS; MASS SPECTROMETRY; METABOLOMICS; QUALITY CONTROL; TIME FACTORS;

EID: 84872531645     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/ac302877x     Document Type: Article

References (29)

1. Robertson, D. G. Toxicol. Sci. 2005, 85, 809-822
2. Weljie, A. M.; Newton, J.; Mercier, P.; Carlson, E.; Slupsky, C. M. Anal. Chem. 2006, 78, 4430-4442
3. Castillo, S.; Gopalacharyulu, P.; Yetukuri, L.; Orešič, M. Chemom. Intell. Lab. Syst. 2011, 108, 23-32
4. van der Kloet, F. M.; Bobeldijk, I.; Verheij, E. R.; Jellema, R. H. J. Proteome Res. 2009, 8, 5132-5141
5. Leek, J. T.; Scharpf, R. B.; Bravo, H. C.; Simcha, D.; Langmead, B.; Johnson, W. E.; Geman, D.; Baggerly, K.; Irizarry, R. A. Nat. Rev. Genet. 2010, 11, 733-739
6. 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
7. Redestig, H.; Fukushima, A.; Stenlund, H.; Moritz, T.; Arita, M.; Saito, K.; Kusano, M. Anal. Chem. 2009, 81, 7974-7980
8. van den Berg, R. A.; Hoefsloot, H. C.; Westerhuis, J. A.; Smilde, A. K.; van der Werf, M. J. BMC Genomics 2006, 7, 142
9. Luo, J.; Schumacher, M.; Scherer, A.; Sanoudou, D.; Megherbi, D.; Davison, T.; Shi, T.; Tong, W.; Shi, L.; Hong, H.; Zhao, C.; Elloumi, F.; Shi, W.; Thomas, R.; Lin, S.; Tillinghast, G.; Liu, G.; Zhou, Y.; Herman, D.; Li, Y.; Deng, Y.; Fang, H.; Bushel, P.; Woods, M.; Zhang, J. Pharmacogenomics J. 2010, 10, 278-291
10. Callister, S. J.; Barry, R. C.; Adkins, J. N.; Johnson, E. T.; Qian, W.-j.; Webb-Robertson, B.-J. M.; Smith, R. D.; Lipton, M. S. J. Proteome Res. 2006, 5, 277-286
11. Xia, J.; Psychogios, N.; Young, N.; Wishart, D. S. Nucleic Acids Res. 2009, 37, W652-660
12. Bolstad, B. M.; Irizarry, R. A.; Astrand, M.; Speed, T. P. Bioinformatics 2003, 19, 185-193
13. 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
14. Quackenbush, J. Nat. Genet. 2002, 32 (Suppl) 496-501
15. Kamleh, M. A.; Ebbels, T. M. D.; Spagou, K.; Masson, P.; Want, E. J. Anal. Chem. 2012, 84, 2670-2677
16. 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
17. Yan, Y.; Weaver, V. M.; Blair, I. A. J. Proteome Res. 2005, 4, 2007-2014
18. Isao, N. J. Mol. Struct. 2008, 883-884, 216-227
19. Smilde, A. K.; van der Werf, M. J.; Bijlsma, S.; van der Werff-van der Vat, B. J. C.; Jellema, R. H. Anal. Chem. 2005, 77, 6729-6736
20. Pluskal, T.; Castillo, S.; Villar-Briones, A.; Oresic, M. BMC Bioinf. 2010, 11, 395
21. Wang, W.; Zhou, H.; Lin, H.; Roy, S.; Shaler, T. A.; Hill, L. R.; Norton, S.; Kumar, P.; Anderle, M.; Becker, C. H. Anal. Chem. 2003, 75, 4818-4826
22. Crawford, L. R.; Morrison, J. D. Anal. Chem. 1968, 40, 1464-1469
23. Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. Mol. Syst. Biol. 2005, 1, 2005-0017
24. Smith, C. A.; Want, E. J.; O'Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779-787
25. Tautenhahn, R.; Bottcher, C.; Neumann, S. BMC Bioinf. 2008, 9, 504
26. R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria, http://www.R-project.org, 2010.
27. Richard, M. S. Using the GNU Compiler Collection. Boston, http://gcc.gnu.org, 2010.
28. FDA. Guidance for Industry, Bioanalytical Method Validation, Food and Drug Administration, Centre for Drug Valuation and Research (CDER), May 2001.
29. Wong, M. C.; Lee, W. T.; Wong, J. S.; Frost, G.; Lodge, J. J. Chromatogr., B 2008, 871, 341-348