Critical aspects of urine profiling for the selection of potential biomarkers using UPLC-TOF-MS

Biomedical Chromatography

Volumn 26, Issue 4, 2012, Pages 512-517

  Mattarucchi, Elia ^a   Guillou, Claude ^a  

^a JOINT RESEARCH CENTRE   (Italy)

Author keywords

'peak picking'; Biomarker selection; Metabolomics; Missing data; Urine profiling

Indexed keywords

BODY FLUIDS; METABOLISM;

'PEAK-PICKING'; BIOMARKER SELECTIONS; CRITICAL FACTORS; METABOLIC PROFILES; METABOLOMICS; MISSING DATA; MISSING VALUES; PEAK PICKING; UPLC/TOF MS; URINE PROFILING;

BIOMARKERS;

BIOLOGICAL MARKER;

ARTICLE; CONCENTRATION (PARAMETERS); DILUTION; HUMAN; MALE; METABOLOMICS; NORMAL HUMAN; SPIKE; TIME OF FLIGHT MASS SPECTROMETRY; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY TIME OF FLIGHT MASS SPECTROMETRY; URINALYSIS;

EID: 84858005763     PISSN: 02693879     EISSN: 10990801     Source Type: Journal    
DOI: 10.1002/bmc.1697     Document Type: Article

References (19)

1. Boccard J, Veuthey JL and Rudaz S. Knowledge discovery in metabolomics: an overview of MS data handling. Journal of Separation Science 2010; 33: 290-304.
2. Brodsky L, Moussaieff A, Shahaf N, Aharoni A and Rogachev I. Evaluation of peak picking quality in LC-MS metabolomics data. Analytical Chemistry 2010; 82: 9177-9187.
3. Dunn WB, Broadhurst D, Brown M, Baker PN, Redman CW, Kenny LC and Kell DB. Metabolic profiling of serum using ultra performance liquid chromatography and the LTQ-Orbitrap mass spectrometry system. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Science 2008; 871: 288-298.
4. Gika HG, Macpherson E, Theodoridis GA and Wilson ID. Evaluation of the repeatability of ultra-performance liquid chromatography-TOF-MS for global metabolic profiling of human urine samples. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Science 2008; 871: 299-305.
5. Katajamaa M and Oresic M. Data processing for mass spectrometry-based metabolomics. Journal of Chromatography. A 2007; 1158: 318-328.
6. Kind T and Fiehn O. Advances in structure elucidation of small molecules using mass spectrometry. Bioanalytical Reviews 2010; 2: 23-60.
7. Legido-Quigley C, Stella C, Perez-Jimenez F, Lopez-Miranda J, Ordovas J, Powell J, van-der-Ouderaa F, Ware L, Lindon JC, Nicholson JK and Holmes E. Liquid chromatography-mass spectrometry methods for urinary biomarker detection in metabonomic studies with application to nutritional studies. Biomedical Chromatography 2010; 24: 737-743.
8. Mattarucchi E, Stocchero M, Moreno-Rojas JM, Giordano G, Reniero F and Guillou C. Authentication of trappist beers by LC-MS fingerprints and multivariate data analysis. Journal of Agricultural and Food Chemistry 2010; 58: 12089-12095.
9. Mattarucchi E, Baraldi E and Guillou C. Metabolomics applied to urine samples in childhood asthma; differentiation between asthma phenotypes and identification of relevant metabolites. Biomedical Chromatography 2011; doi: 10.1002/bmc.1631
10. Pandher R, Ducruix C, Eccles SA and Raynaud FI. Cross-platform Q-TOF validation of global exo-metabolomic analysis: application to human glioblastoma cells treated with the standard PI 3-Kinase inhibitor LY294002. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Science 2009; 877: 1352-1358.
11. Ryan D, Robards K, Prenzler PD and Kendall M. Recent and potential developments in the analysis of urine: a review. Analytica Chimica Acta 2011; 684: 8-20.
12. Scalbert A, Brennan L, Fiehn O, Hankemeier T, Kristal BS, van Ommen B, Pujos-Guillot E, Verheij E, Wishart D and Wopereis S. Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics 2009; 5: 435-458.
13. Trygg J, Holmes E and Lundstedt T. Chemometrics in metabonomics. Journal of Proteome Research 2007; 6: 469-479.
14. Veselkov KA, Vingara LK, Masson P, Robinette SL, Want E, Li JV, Barton RH, Boursier-Neyret C, Walther B, Ebbels TM, Pelczer I, Holmes E, Lindon JC and Nicholson JK. Optimized pre-processing of UPLC-MS urinary metabolic profiles for improved information recovery. Analytical Chemistry 2011; 83: 5864-5872.
15. Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, Shockcor J, Holmes E and Nicholson JK. Global metabolic profiling procedures for urine using UPLC-MS. Nature Protocols 2010; 5: 1005-1018.
16. Warrack BM, Hnatyshyn S, Ott KH, Reily MD, Sanders M, Zhang H and Drexler DM. Normalization strategies for metabonomic analysis of urine samples. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Science 2009; 877: 547-552.
17. Waters. Controlling contamination in ultraperformance LC/MS systems, 2005. Available from (accessed 12 May 2009).
18. Wiklund S, Johansson E, Sjöström L, Mellerowicz EJ, Edlund U, Shockcor PJ, Gottfries J, Moritz T and Trygg J. Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models. Analytical Chemistry 2008; 80: 115-122.
19. Wong MC, Lee WT, Wong JS, Frost G and Lodge J. An approach towards method development for untargeted urinary metabolite profiling in metabonomic research using UPLC/QTOF MS. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Science 2008; 871: 341-348.