Global metabolic profiling procedures for urine using UPLC-MS

Nature Protocols

Volumn 5, Issue 6, 2010, Pages 1005-1018

  Want, Elizabeth J ^a   Wilson, Ian D ^b   Gika, Helen ^c   Theodoridis, Georgios ^c   Plumb, Robert S ^d   Shockcor, John ^d   Holmes, Elaine ^a   Nicholson, Jeremy K ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b ASTRAZENECA   (United Kingdom)

^c ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^d WATERS CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

ARTICLE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; INFORMATION PROCESSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUALITY CONTROL; SEPARATION TECHNIQUE; STORAGE; URINALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ELECTROSPRAY MASS SPECTROMETRY; METABOLOME; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROCEDURES; URINE;

BIOLOGICAL MARKERS; CHROMATOGRAPHY, LIQUID; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; METABOLOME; METABOLOMICS; MOLECULAR STRUCTURE; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; URINE;

EID: 77952205557     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2010.50     Document Type: Article

References (79)

1. Nicholson, J.K., Lindon, J.C. & Holmes, E. Metabonomics: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29, 1181-1189 (1999).
2. Nicholson, J.K., Connelly, J., Lindon, J.C. & Holmes, E. Metabonomics: a platform for studying drug toxicity and gene function. Nat. Rev. Drug Discov. 1, 153-161 (2002). (Pubitemid 41646523)
3. Fiehn, O. Metabolomics-the link between genotypes and phenotypes. Plant. Mol. Biol. 48, 155-171 (2002).
4. Nicholson, J.K. & Lindon, J.C. Systems biology: metabonomics. Nature 455, 1054-1056 (2008).
5. Wishart, D.S. Applications of metabolomics in drug discovery and development. Drugs R. D. 9, 307-322 (2008).
6. Clarke, C.J. & Haselden, J.N. Metabolic profiling as a tool for understanding mechanisms of toxicity. Toxicol. Pathol. 36, 140-147 (2008).
7. Bollard, M.E. et al. Comparative metabonomics of differential hydrazine toxicity in the rat and mouse. Toxicol. Appl. Pharmacol. 204, 135-151 (2005).
8. Lindon, J.C., Holmes, E. & Nicholson, J.K. Metabonomics in pharmaceutical R&D. FEBS J. 274, 1140-1151 (2007).
9. Coen, M., Holmes, E., Lindon, J.C. & Nicholson, J.K. NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem. Res. Toxicol. 21, 9-27 (2008). (Pubitemid 351219705)
10. Hinkelbein, J. et al. Alterations in cerebral metabolomics and proteomic expression during sepsis. Curr. Neurovasc. Res. 4, 280-288 (2007). (Pubitemid 350171829)
11. Bertini, I. et al. The metabonomic signature of celiac disease. J. Proteome. Res. 8, 170-177 (2009).
12. Gowda, G.A. et al. Metabolomics-based methods for early disease diagnostics. Expert. Rev. Mol. Diagn. 8, 617-633 (2008).
13. Lenz, E.M. et al. Metabonomics, dietary influences and cultural differences: a 1H NMR-based study of urine samples obtained from healthy British and Swedish subjects. J. Pharm. Biomed. Anal. 36, 841-849 (2004).
14. Gieger, C. et al. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet. 4, e1000282 (2008).
15. Holmes, E. et al. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453, 396-400 (2008). (Pubitemid 351693125)
16. Beckonert, O. et al. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat. Protoc. 2, 2692-2703 (2007).
17. Gika, H.G., Theodoridis, G. & Wilson, I.D. 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 (2008).
18. Want, E.J. et al. Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal. Chem. 78, 743-752 (2006).
19. Michopoulos, F., Lai, L., Gika, H., Theodoridis, G. & Wilson, I.D. UPLC-MSbased analysis of human plasma for metabonomics using solvent precipitation or solid phase extraction. J. Proteome. Res. 8, 2114-2121 (2009).
20. Zelena, E. et al. Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum. Anal. Chem. 81, 1357-1364 (2009).
21. Barton, R.H., Nicholson, J.K., Elliott, P. & Holmes, E. High-throughput 1H NMR-based metabolic analysis of human serum and urine for large-scale epidemiological studies: validation study. Int. J. Epidemiol. 37 (Suppl 1): i31-i40 (2008).
22. Lauridsen, M., Hansen, S.H., Jaroszewski, J.W. & Cornett, C. Human urine as test material in 1H NMR-based metabonomics: recommendations for sample preparation and storage. Anal. Chem. 79, 1181-1186 (2007). (Pubitemid 46254423)
23. Matuszewski, B.K., Constanzer, M.L. & Chavez-Eng, C.M. Matrix effect in quantitative LC/MS/MS analyses of biological fluids: a method for determination of finasteride in human plasma at picogram per milliliter concentrations. Anal. Chem. 70, 882-889 (1998). (Pubitemid 128494097)
24. Gangl, E.T., Annan, M.M., Spooner, N. & Vouros, P. Reduction of signal suppression effects in ESI-MS using a nanosplitting device. Anal. Chem. 73, 5635-5644 (2001). (Pubitemid 33126718)
25. Gustavsson, S.A., Samskog, J., Markides, K.E. & Långström, B. Studies of signal suppression in liquid chromatography-electrospray ionization mass spectrometry using volatile ion-pairing reagents. J. Chromatogr. A 937, 41-47 (2001). (Pubitemid 33079154)
26. Jellum, E. Profiling of human body fluids in healthy and diseased states using gas chromatography and mass spectrometry, with special reference to organic acids. J. Chromatogr. 143, 427-462 (1977).
27. Taylor, N.F. Urinary steroid profiling. Methods Mol. Biol. 324, 159-175 (2006).
28. Halket, J.M et al. Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J. Exp. Botany 56, 219-243 (2005).
29. New, L.S. & Chan, E.C. Evaluation of BEH C18, BEH HILIC, and HSS T3 (C18) column chemistries for the UPLC-MS-MS analysis of glutathione, glutathione disulfide, and ophthalmic acid in mouse liver and human plasma. J. Chromatogr. Sci. 46, 209-214 (2008).
30. Wilson, I.D. et al. High resolution ultra performance liquid chromatography coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J. Proteome. Res. 4, 591-598 (2005).
31. Tolstikov, V.V. & Fiehn, O. Analysis of highly polar compounds of plant origin: combination of hydrophilic interaction chromatography and electrospray ion trap mass spectrometry. Anal. Biochem. 301, 298-307 (2002). (Pubitemid 34158194)
32. Idborg, H., Zamani, L., Schuppe-Koistinen, I. & Jacobsson, S. Metabolic fingerprinting of rat urine by LC/MS Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry. J. Chromatogr. B 828, 9-13 (2005). (Pubitemid 41735293)
33. Cubbon, S., Bradbury, T., Wilson, J. & Thomas-Oates, J. Hydrophilic interaction chromatography for mass spectrometric metabonomic studies of urine. Anal. Chem. 79, 8911-8918 (2007). (Pubitemid 350231697)
34. Gika, H.G., Theodoridis, G.A. & Wilson, I.D. Hydrophilic interaction and reversed-phase ultra-performance liquid chromatography TOF-MS for metabonomic analysis of Zucker rat urine. J. Sep. Sci. 31, 1598-1608 (2008).
35. Plumb, R.S. et al. A rapid screening approach to metabonomics using UPLC and oa-TOF mass spectrometry: application to age, gender and diurnal variation in normal/Zucker obese rats and black, white and nude mice. Analyst 130, 844-849 (2005).
36. Kind, T., Tolstikov, V., Fiehn, O. & Weiss, R.H. A comprehensive urinary metabolomic approach for identifying kidney cancer. Anal. Biochem. 363, 185-195 (2007). (Pubitemid 46428214)
37. Guy, P.A., Tavazzi, I., Bruce, S.J., Ramadan, Z. & Kochhar, S. 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 (2008).
38. Plumb, R.S. et al. Generation of ultrahigh peak capacity LC separations via elevated temperatures and high linear mobile-phase velocities. Anal. Chem. 78, 7278-7283 (2006).
39. Gika, H.G., Theodoridis, G., Extance, J., Edge, A.M. & Wilson, I.D. High temperature-ultraperformance liquid chromatography-mass spectrometry for the metabonomic analysis of Zucker rat urine. J. Chrom. B. 871, 279-287 (2008). (Pubitemid 351890787)
40. Lenz, E.M., Bright, J., Knight, R., Wilson, I.D. & Major, H. A metabonomic investigation of the biochemical effects of mercuric chloride in the rat using 1H NMR and HPLC-TOF/MS: time dependant changes in the urinary profile of endogenous metabolites as a result of nephrotoxicity. Analyst 129, 535-541 (2004). (Pubitemid 38813520)
41. Nordström, A., Want, E., Northen, T., Lehtiö, J. & Siuzdak, G. Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics. Anal. Chem. 80, 421-429 (2008).
42. Leandro, C.C., Hancock, P., Fussell, R.J. & Keely, B.J. Ultra-performance liquid chromatography for the determination of pesticide residues in foods by tandem quadrupole mass spectrometry with polarity switching. J. Chromatogr. A 1144, 161-169 (2007). (Pubitemid 46298855)
43. Want, E.J., Nordström, A., Morita, H. & Siuzdak, G. From exogenous to endogenous: the inevitable imprint of mass spectrometry in metabolomics. J. Proteome. Res. 6, 459-468 (2007). (Pubitemid 46340150)
44. Plumb, R.S. et al. UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun. Mass Spectrom. 20, 1989-1994 (2006).
45. Bateman, K.P. et al. MSE with mass defect filtering for in vitro and in vivo metabolite identification. Rapid Commun. Mass Spectrom. 21, 1485-1496 (2007).
46. Crockford, D.J. 1H NMR and UPLC-MS(E) statistical heterospectroscopy: characterization of drug metabolites (xenometabolome) in epidemiological studies. Anal. Chem. 80, 6835-6844 (2008).
47. Perry, R.H., Cooks, R.G. & Noll, R.J. Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom. Rev. 27, 661-699 (2008).
48. Gika, H.G., Theodoridis, G.A., Wingate, J.E. & Wilson, I.D. Within day reproducibility of an HPLC-MS-based method for metabonomic analysis: application to human urine. J. Proteome. Res. 6, 3291-3303 (2007).
49. Gika, H.G., Macpherson, E., Theodoridis, G. & Wilson, I.D. Evaluation of the repeatability of ultra-performance liquid chromatography-TOF-MS for global metabolic profiling of human urine samples. J. Chromatogr. B 871, 299-305 (2008).
50. Baker, J.M. et al. A metabolomic study of substantial equivalence of fieldgrown genetically modified wheat. Plant Biotechnol. J. 4, 381-392 (2006).
51. Sangster, T., Major, H., Plumb, R., Wilson, A.J. & Wilson, I.D. A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MSbased metabonomic analysis. Analyst 131, 1075-1078 (2006). (Pubitemid 44465534)
52. FDA Guidance for Industry, Bioanalytical method Validation, Food and Drug Administration, Centre for Drug Evaluation and Research (CDER), May 2001.
53. Viswanathan, C.T. et al. Quantitative bioanalytical methods validation and implementation: best practices for chromatographic and ligand binding assays. Pharm. Res. 24, 1962-1973 (2007). (Pubitemid 47389236)
54. Pham-Tuan, H., Kaskavelis, L., Daykin, C.A. & Janssen, H. Method development in high-performance liquid chromatography for highthroughput profiling and metabonomic studies of biofluid samples. J. Chromatogr. B 789, 283-301 (2003). (Pubitemid 36549198)
55. Smith, C.A., Want, E.J., OMaille, G., Abagyan, R. & Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779-787 (2006). (Pubitemid 43228585)
56. Katajamaa, M., Miettinen, J. & Oresic, M. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22, 634-636 (2006). (Pubitemid 43372832)
57. Duran, A.L., Yang, J., Wang, L.J. & Sumner, L.W. Metabolomics spectral formatting, alignment and conversion tools (MSFACTs). Bioinformatics 19, 2283-2293 (2003). (Pubitemid 37483984)
58. Baran, R. et al. MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics 7, 530-538 (2006). (Pubitemid 46024016)
59. Broeckling, C.D., Reddy, I.R., Duran, A.L., Zhao, X.C. & Sumner, L.W. MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Anal. Chem. 78, 4334-4341 (2006).
60. Katajamaa, M. & Oresic, M.J. Data processing for mass spectrometry-based metabolomics. Chromatogr. A 1158, 318-328 (2007). (Pubitemid 47021150)
61. Sumner, L.W., Urbanczyk-Wochniak, E. & Broeckling, C.D. Metabolomics data analysis, visualization, and integration. Methods Mol. Biol. 406, 409-436 (2007). (Pubitemid 351367185)
62. Ruan, Q. et al. An integrated method for metabolite detection and identification using a linear ion trap/Orbitrap mass spectrometer and multiple data processing techniques: application to indinavir metabolite detection. J. Mass. Spectrom. 43, 251-261 (2008). (Pubitemid 351303446)
63. Zhang, N.R. et al. Quantitation of small molecules using high-resolution accurate mass spectrometers-a different approach for analysis of biological samples. Rapid Commun. Mass Spectrom. 23, 1085-1094 (2009).
64. Ohta, D., Shibata, D. & Kanaya, S. Metabolic profiling using Fouriertransform ion-cyclotron-resonance mass spectrometry. Anal. Bioanal. Chem. 389, 1469-1475 (2007). (Pubitemid 350023671)
65. Crockford, D.J. et al. Statistical heterospectroscopy, an approach to the integrated analysis of NMR and UPLC-MS data sets: application in metabonomic toxicology studies. Anal. Chem. 78, 363-371 (2006).
66. Wishart, D.S. et al. HMDB: the human metabolome database. Nucleic Acids Res. 35 (Database issue): D521-D526 (2007).
67. Wishart, D.S. et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 37 (Database issue): D603-D610 (2009).
68. Smith, C.A. et al. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27, 747-751 (2005).
69. Draper, J. et al. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour rules. BMC Bioinformatics 10, 227 (2009).
70. Wilson, I.D. & Nicholson, J.K. Solid-phase extraction chromatography and nuclear magnetic resonance spectroscopy for the identification and isolation of drug metabolites in urine. Anal. Chem. 59, 2830-2832 (1987).
71. Baranyi, M., Milusheva, E., Vizi, E.S. & Sperlágh, B. Chromatographic analysis of dopamine metabolism in a Parkinsonian model. J. Chromatogr. A 1120, 13-20 (2006). (Pubitemid 43866771)
72. Gavaghan, C.L. et al. Directly coupled high-performance liquid chromatography and nuclear magnetic resonance spectroscopy with chemometric studies on metabolic variation in Sprague-Dawley rats. Anal. Biochem. 291, 245-252 (2001).
73. Spraul, M., Hofmann, M., Dvortsack, P., Nicholson, J.K. & Wilson, I.D. High-performance liquid chromatography coupled to high-field proton nuclear magnetic resonance spectroscopy: application to the urinary metabolites of ibuprofen. Anal. Chem. 65, 327-330 (1993). (Pubitemid 23087025)
74. Dear, G.J. et al. Mass directed peak selection, an efficient method of drug metabolite identification using directly coupled liquid chromatography-mass spectrometry-nuclear magnetic resonance spectroscopy. J. Chromatogr. B Biomed. Sci. Appl. 748, 281-293 (2000).
75. Lin, Y., Schiavo, S., Orjala, J., Vouros, P. & Kautz, R. Microscale LC-MSNMR platform applied to the identification of active cyanobacterial metabolites. Anal. Chem. 80, 8045-8054 (2008).
76. Shockcor, J.P. et al. Combined HPLC, NMR spectroscopy, and Ion-trap mass spectrometry with application to the detection and characterisation of xenobiotic and endogenous metabolites in human urine. Anal. Chem. 68, 4431-4435 (1996). (Pubitemid 27006895)
77. Nicholls, A.W, Wilson, I.D., Godejohann, M., Nicholson, J.K. & Shockcor, J.P. Identification of phenacetin metabolites in human urine after administration of phenacetin-C2H3: measurement of futile metabolic deacetylation via HPLC/MS-SPE-NMR and HPLC-ToF MS. Xenobiotica 36, 615-629 (2006). (Pubitemid 44174448)
78. Spraul, M. et al. Advancing NMR sensitivity for LC-NMR-MS using a cryoflow probe: application to the analysis of acetaminophen metabolites in urine. Anal. Chem. 75, 1536-1541 (2003). (Pubitemid 36397188)
79. Shockcor, J.P., Unger, S.E., Savina, P., Nicholson, J.K. & Lindon, J.C. Application of directly coupled LC-NMR-MS to the structural elucidation of metabolites of the HIV-1 reverse-transcriptase inhibitor BW935U83. J. Chromatogr. B Biomed. Sci. Appl. 748, 269-279 (2000).