Metabolomics data normalization with EigenMS

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Karpievitch, Yuliya V ^a   Nikolic, Sonja B ^b   Wilson, Richard ^c   Sharman, James E ^c   Edwards, Lindsay M ^d,e  

^a UNIVERSITY OF TASMANIA   (Australia)

^b UNIVERSITY OF TASMANIA   (Australia)

^c UNIVERSITY OF TASMANIA   (Australia)

^d KING'S COLLEGE LONDON   (United Kingdom)

^e GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHOLESTEROL; GLYCOSYLATED HEMOGLOBIN;

ADULT; ARTICLE; CHOLESTEROL BLOOD LEVEL; CLINICAL ARTICLE; CONTROLLED STUDY; EIGENMS; GLUCOSE BLOOD LEVEL; HEART RATE; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; MIDDLE AGED; NON INSULIN DEPENDENT DIABETES MELLITUS; PROTEIN DATABASE; SENSITIVITY AND SPECIFICITY; STATISTICAL BIAS; TREATMENT OUTCOME; AGED; BLOOD; FACTUAL DATABASE; METABOLISM; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

AGED; CHROMATOGRAPHY, LIQUID; DATABASES, FACTUAL; DIABETES MELLITUS, TYPE 2; HUMANS; MASS SPECTROMETRY; METABOLOMICS; MIDDLE AGED; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84920158793     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116221     Document Type: Article

References (15)

1. Zelena E, Dunn WB, Broadhurst D, Francis-McIntyre S, Carroll KM, et al. (2009) Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal Chem 81: 1357-1364.
2. Gika HG, Theodoridis GA, Wilson ID (2008) Liquid chromatography and ultra-performance liquid chromatography-mass spectrometry fingerprinting of human urine: sample stability under different handling and storage conditions for metabonomics studies. J Chromatogr A 1189: 314-322.
3. Guy PA, Tavazzi I, Bruce SJ, Ramadan Z, Kochhar S (2008) Global metabolic profiling analysis on human urine by UPLC-TOFMS: issues and method validation in nutritional metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 871: 253-260.
4. Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, et al. (2012) Model-driven multiomic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol 8: 558.
5. Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, et al. (2013) A Multi-Omic View of Host-Pathogen-Commensal Interplay in -Mediated Intestinal Infection. PLoS One 8: e67155.
6. Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, et al. (2013) Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst 9: 1522-1534.
7. Metz TO, Page JS, Baker ES, Tang K, Ding J, et al. (2008) High Resolution Separations and Improved Ion Production and Transmission in Metabolomics. Trends Analyt Chem 27: 205-214.
8. Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, et al. (2010) Global metabolic profiling procedures for urine using UPLC-MS. Nature Protocols 5: 1005-1018.
9. Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, et al. (2009) Normalization of Peak Intensities in Bottom-Up MS-Based Proteomics Using Singular Value Decomposition. Bioinformatics 25: 2573-2580.
10. Nikolic S, Wilson R, Hare J, Adams M, Edwards L, et al. (2014) Spironolactone reduces aortic stiffness via blood pressure-dependent effects of canrenoate. Metabolomics 10: 105-113.
11. 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 metabolomic analysis. The Analyst 131: 1075-1078.
12. Leek JT, Storey JD (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics 3.
13. Lai L, Michopoulos F, Gika H, Theodoridis G, Wilkinson RW, et al. (2010) Methodological considerations in the development of HPLC-MS methods for the analysis of rodent plasma for metabonomic studies. Mol Biosyst 6: 108-120.
14. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society 57: 289-300.
15. Climie RED, Nikolic SB, Otahal P, Keith LJ, Sharman JE (2013) Augmentation index and arterial stiffness in patients with type 2 diabetes mellitus. Artery Research 7: 194-200.