Batch profiling calibration for robust NMR metabonomic data analysis

Analytical and Bioanalytical Chemistry

Volumn 405, Issue 27, 2013, Pages 8819-8827

  Fages, Anne ^a   Pontoizeau, Clément ^a   Jobard, Elodie ^a   Lévy, Pierre ^b   Bartosch, Birke ^a   Elena Herrmann, Bénédicte ^a  

^a UNIVERSITÉ DE LYON   (France)

^b CENTRE DE RECHERCHE EN CANCÉROLOGIE DE LYON   (France)

Author keywords

Batch calibration; Batch profiling; Metabolomics; Metabonomics; NMR

Indexed keywords

CALIBRATION; DATA ACQUISITION; DISCRIMINANT ANALYSIS; MULTIVARIANT ANALYSIS; NUCLEAR MAGNETIC RESONANCE;

BATCH PROFILING; BIOLOGICAL VARIABILITY; EPIDEMIOLOGICAL STUDIES; METABOLIC FINGERPRINTS; METABOLOMICS; METABONOMICS; MULTIVARIATE STATISTICAL MODELS; NUCLEAR MAGNETIC RESONANCE(NMR);

QUALITY CONTROL;

ARTICLE; BLOOD; CALIBRATION; CRYOPRESERVATION; HEALTH CARE FACILITY; HUMAN; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE; PANCREAS TUMOR; PRINCIPAL COMPONENT ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY; STANDARD; STATISTICAL MODEL; STATISTICS;

BIOLOGICAL SPECIMEN BANKS; CALIBRATION; CRYOPRESERVATION; HUMANS; METABOLOMICS; MODELS, STATISTICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PANCREATIC NEOPLASMS; PRINCIPAL COMPONENT ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS;

EID: 84893704082     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-013-7296-0     Document Type: Article

References (35)

1. Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL (2011) Systems level studies of mammalian metabolomes: The roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem Soc Rev 40(1):387-426
2. Suhre K, Shin SY, Petersen AK,Mohney RP, Meredith D,Wagele B, Altmaier E, Deloukas P, Erdmann J, Grundberg E, Hammond CJ, de Angelis MH, Kastenmuller G, Kottgen A, Kronenberg F, Mangino M, Meisinger C, Meitinger T, Mewes HW, Milburn MV, Prehn C, Raffler J, Ried JS, Romisch-Margl W, Samani NJ, Small KS, Wichmann HE, Zhai GJ, Illig T, Spector TD, Adamski J, Soranzo N, Gieger C, (2011) Human metabolic individuality in biomedical and pharmaceutical research. Nature 477(7362):54-60
3. Gieger C, Geistlinger L, Altmaier E, de Angelis MH, Kronenberg F, Meitinger T,Mewes HW,Wichmann HE,Weinberger KM, Adamski J, Illig T, Suhre K (2008) Genetics meets metabolomics: A genomewide association study of metabolite profiles in human serum. PLoS Genet 4(11
4. Bao YQ, Zhao T, Wang XY, Qiu YP, Su MM, Jia WP, Jia W (2009) Metabonomic variations in the drug-treated type 2 diabetes mellitus patients and healthy volunteers. J Proteome Res 8(4):1623-1630
5. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu JD, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao XH, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM (2009) Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457(7231):910-914
6. Gibney MJ, Walsh M, Brennan L, Roche HM, German B, van Ommen B (2005) Metabolomics in human nutrition: Opportunities and challenges. Am J Clin Nutrit 82(3):497-503
7. Teahan O, Gamble S, Holmes E,Waxman J, Nicholson JK, Bevan C, Keun HC (2006) Impact of analytical bias in metabonomic studies of human blood serum and plasma. Anal Chem 78(13):4307-4318
8. Gika HG, Theodoridis GA,Wingate JE,Wilson ID (2007)Within-day reproducibility of an HPLC-MS-Based method for metabonomic analysis: Application to human urine. J Proteome Res 6(8):3291-3303
9. Gika HG,Macpherson E, TheodoridisGA,Wilson ID (2008) Evaluation of the repeatability of ultra-performance liquid chromatography-TOFMS for global metabolic profiling of human urine samples. J Chromatogr, B: Anal Technol Biomed Life Sci 871(2):299-305
10. Lai L, Michopoulos F, Gika H, Theodoridis G,Wilkinson RW, Odedra R, Wingate J, Bonner R, Tate S, Wilson ID (2010) Methodological considerations in the development of HPLC-MS methods for the analysis of rodent plasma for metabonomic studies. Mol Biosyst 6(1):108-120
11. Wagner S, Scholz K, SieberM, Kellert M, VoelkelW(2007) Tools in metabonomics: An integrated validation approach for LC-MS metabolic profiling of mercapturic acids in human urine. Anal Chem 79(7):2918-2926
12. Sangster T, Major H, Plumb R, Wilson AJ, Wilson ID (2006) A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MS-based metabonomic analysis. Analyst 131(10):1075-1078
13. Dunn WB, Broadhurst D, Begley P, Zelena E, Francis-McIntyre S, Anderson N, Brown M, Knowles JD, Halsall A, Haselden JN, Nicholls AW, Wilson ID, Kell DB, Goodacre R (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6(7):1060-1083
14. van der Greef J, Martin S, Juhasz P, Adourian A, Plasterer T, Verheij ER, McBurney RN (2007) The art and practice of systems biology in medicine: Mapping patterns of relationships. J Proteome Res 6(4):1540-1559
15. Zelena E,DunnWB, Broadhurst D, Francis-McIntyre S, Carroll KM, Begley P, O'Hagan S, Knowles JD, Halsall A, Wilson ID, Kell DB (2009) Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal Chem 81(4):1357-1364
16. Wang SY, Kuo CH, Tseng YJ (2013) Batch Normalizer: A fast total abundance regression calibration method to simultaneously adjust batch and injection order effects in liquid chromatography/time-offlight mass spectrometry-based metabolomics data and comparison with current calibration methods. Anal Chem 85(2):1037-1046
17. Kirwan JA, Broadhurst DI, Davidson RL, Viant MR (2013) Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow. Anal Bioanal Chem 405(15):5147-5157
18. Kamleh MA, Ebbels TM, Spagou K, Masson P, Want EJ (2012) Optimizing the use of quality control samples for signal drift correction in large-scale urine metabolic profiling studies. Anal Chem 84(6):2670-2677
19. van der Kloet FM, Bobeldijk I, Verheij ER, Jellema RH (2009) Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping. J Proteome Res 8(11):5132-5141
20. Sysi-Aho M, Katajamaa M, Yetukuri L, Oresic M (2007) Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinforma 8:93
21. De Livera AM, Dias DA, De Souza D, Rupasinghe T, Pyke J, Tull D, Roessner U, McConville M, Speed TP (2012) Normalizing and integrating metabolomics data. Anal Chem 84(24):10768-10776
22. Dumas ME, Maibaum EC, Teague C, Ueshima H, Zhou B, Lindon JC, Nicholson JK, Stamler J, Elliott P, Chan Q, Holmes E (2006) Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: The INTERMAP Study. Anal Chem 78(7):2199-2208
23. Blaise BJ, Giacomotto J, TribaMN, Toulhoat P, PiottoM, Emsley L, Segalat L, Dumas ME, Elena B (2009) Metabolic profiling strategy of Caenorhabditis elegans by whole-organism nuclear magnetic resonance. J Proteome Res 8(5):2542-2550
24. Beckonert O, Keun HC, Ebbels TMD, Bundy JG, Holmes E, Lindon JC, Nicholson JK (2007) Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2(11):2692-2703
25. Broadhurst DI, KellDB(2006) Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics 2(4):171-196
26. Lindon JC, Nicholson JK, Holmes E, Keun HC, Craig A, Pearce JTM, Bruce SJ, HardyN, Sansone SA, Antti H, Jonsson P, Daykin C, Navarange M, Beger RD, Verheij ER, Amberg A, Baunsgaard D, Cantor GH, Lehman-McKeeman L, Earll M, Wold S, Johansson E, Haselden JN, Kramer K, Thomas C, Lindberg J, Schuppe-Koistinen I, Wilson ID, Reily MD, Robertson DG, Senn H, Krotzky A, Kochhar S, Powell J, van der Ouderaa F, Plumb R, Schaefer H, Spraul M, worki SMRS (2005) Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23(7):833-838
27. Dunn WB, Wilson ID, Nicholls AW, Broadhurst D (2012) The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans. Bioanalysis 4(18):2249-2264
28. Draisma HHM, Reijmers TH, van der Kloet F, Bobeldijk-Pastorova I, Spies-Faber E, Vogels JTWE, Meulman JJ, Boomsma DI, van der Greef J, Hankemeier T (2010) Equating, or correction for betweenblock effects with application to body fluid LC-MS and NMR metabolomics data sets. Anal Chem 82(3):1039-1046
29. Chu TM, Bao W, Thomas RS, Wolfinger RD (2009) Batch profile estimation, correction, and scoring. In: Scherer A (ed) Batch effects and noise in microarray experiments: Sources and solutions. Wiley, Chichester, pp 155-165
30. Wakita T, Pietschmann T, Kato T, Date T, Miyamoto M, Zhao Z, Murthy K, Habermann A, Krausslich HG, Mizokami M, Bartenschlager R, Liang TJ (2005) Production of infectious hepatitis C virus in tissue culture from a cloned viral genome. Nat Med 11(7):791-796
31. Savorani F, Tomasi G, Engelsen SB (2010) icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. J Magn Reson 202(2):190-202
32. Blaise BJ, Shintu L, Elena B, Emsley L, Dumas ME, Toulhoat P (2009) Statistical recoupling prior to significance testing in nuclear magnetic resonance based metabonomics. Anal Chem 81(15):6242-6251
33. Nicholson JK, Foxall PJD, Spraul M, Farrant RD, Lindon JC (1995) 750-Mhz H-1 and H-1-C-13 Nmr-spectroscopy of human bloodplasma. Anal Chem 67(5):793-811
34. Riboli E, Kaaks R (1997) The EPIC project: Rationale and study design. Int J Epidemiol 26:S6-S14
35. Wold S (1978) Cross-validatory estimation of number of components in factor and principal components models. Technometrics 20(4):397-405