Urine molecular profiling distinguishes health and disease: new methods in diagnostics? Focus on UPLC–MS

References

• Wu X. Urinalysis: a review of methods and procedures. Crit. Care Nurs. Clin. North Am.22, 121–128 (2010).
   Google Scholar
• Hallbach J. [Clinical Chemistry for Beginners]. Georg Thieme Verlag, Stuttgart, Germany, 111 (2001).
   Google Scholar
• Julian BA, Suzuki H, Suzuki Y, Tomino Y, Spasovski G, Novak J. Sources of urinary proteins and their analysis by urinary proteomics for the detection of biomarkers of disease. Proteomics Clin. Appl.3, 1029–1043 (2009).
   PubMed Web of Science ®Google Scholar
• Teunissen SF, Rosing H, Schinkel AH, Schellens JHM, Beijnen JH. Bioanalytical methods for determination of tamoxifen and its Phase I metabolites: a review. Anal. Chim. Acta683, 21–37 (2010).
   PubMed Web of Science ®Google Scholar
• Barroso M, Gallardo E, Queiroz JA. Bioanalytical methods for the determination of cocaine and metabolites in human biological samples. Bioanalysis1, 977–1000 (2009).
   PubMed Web of Science ®Google Scholar
• Janicka M, Kot-Wasik A, Namiesnik J. Analytical procedures for determination of cocaine and its metabolites in biological samples. Trends Analyt. Chem.29, 209–224 (2010).
   Google Scholar
• Taskeen A, Naeem I. Analysis of bisphenol A in blood and urine samples: a mini review. Asian J. Chem.22, 4136–4140 (2010).
   Google Scholar
• Oledzka I, Baczek T. Urinary steroids measured by modern separation techniques and applied as biomarkers in stress studies. Curr. Pharm. Anal.6, 151–163 (2010).
   Google Scholar
• Stanczyk FZ, Clarke NJ. Advantages and challenges of mass spectrometry assays for steroid hormones. J. Steroid Biochem. Mol. Biol.121, 491–495 (2010).
   PubMed Web of Science ®Google Scholar
• Krone N, Hughes BA, Lavery GG, Stewart PM, Arlt W, Shackleton CHL. Gas chromatography/mass spectrometry (GC/MS) remains a pre-eminent discovery tool in clinical steroid investigations even in the era of fast liquid chromatography tandem mass spectrometry (LC/MS/MS). J. Steroid Biochem. Mol. Biol.121, 496–504 (2010).
   PubMed Web of Science ®Google Scholar
• Shrivastav PS, Buha SM, Sanyal M. Detection and quantitation of β-blockers in plasma and urine. Bioanalysis2, 263–276 (2010).
   Google Scholar
• Guichardant M, Lagarde M. Analysis of biomarkers from lipid peroxidation: a comparative study. Eur. J. Lipid Sci. Technol.111, 75–82 (2009).
   Google Scholar
• Dudley E. Analysis of urinary modified nucleosides by mass spectrometry. In: Mass Spectrometry of Nucleosides and Nucleic Acids. JH Banoub, PA Limbach (Eds). CRC Press, FL, USA, 163–194 (2010).
   Google Scholar
• Antonucci R, Atzori L, Barberini L, Fanos V. Metabolomics: the ‘new clinical chemistry’ for personalized neonatal medicine. Minerva Pediatr.62, 145–148 (2010).
   PubMedGoogle Scholar
• Munoz B, Albores A. The role of molecular biology in the biomonitoring of human exposure to chemicals. Int. J. Mol. Sci.11, 4511–4525 (2010).
   PubMed Web of Science ®Google Scholar
• Kim K-B, Lee BM. Metabolomics, a new promising technology for toxicological research. Toxicol. Res.25, 59–69 (2009).
   Google Scholar
• Patterson AD, Lanz C, Gonzalez FJ, Idle JR. The role of mass spectrometry-based metabolomics in medical countermeasures against radiation. Mass Spectrom. Rev.29, 503–521 (2010).
   PubMed Web of Science ®Google Scholar
• Fave G, Beckmann ME, Draper JH, Mathers JC. Measurement of dietary exposure: a challenging problem which may be overcome thanks to metabolomics? Genes Nutr.4, 135–141 (2009).
   PubMed Web of Science ®Google Scholar
• Zhang S, Nagana GGA, Ye T, Raftery D. Advances in NMR-based biofluid analysis and metabolite profiling. Analyst135, 1490–1498 (2010).
   PubMed Web of Science ®Google Scholar
• Wilson ID, Lindon JC, Nicholson JK. The practice of NMR spectroscopy in drug metabolism studies. Drugs Pharm. Sci.186, 373–392 (2009).
   Google Scholar
• Issaq HJ, Van QN, Waybright TJ, Muschik GM, Veenstra TD. Analytical and statistical approaches to metabolomics research. J. Sep. Sci.32, 2183–2199 (2009).
   PubMed Web of Science ®Google Scholar
• Cubbon S, Antonio C, Wilson J, Thomas-Oates J. Metabolomic applications of HILIC–LC–MS. Mass Spectrom. Rev.29, 671–684 (2010).
   PubMed Web of Science ®Google Scholar
• Tsikas D. Quantitative analysis of biomarkers, drugs and toxins in biological samples by immunoaffinity chromatography coupled to mass spectrometry or tandem mass spectrometry: a focused review of recent applications. J. Chromatogr. B Anal. Technol. Biomed. Life Sci.878, 133–148 (2010).
   PubMed Web of Science ®Google Scholar
• Ojanperä I, Pelander A, Ojanperä S. Comprehensive toxicological and forensic drug screening by LC/TOF-MS, in liquid chromatography time-of-flight mass spectrometry. In: Principles, Tools, and Applications for Accurate Mass Analysis. Ferrer I, Thurman EM (Eds). John Wiley & Sons, Inc., NJ, USA, 173, 179–195 (2008).
   Google Scholar
• Ramautar R, Somsen GW, De Jong GJ. CE–MS in metabolomics. Electrophoresis30, 276–291 (2009).
   PubMed Web of Science ®Google Scholar
• Kentsis A, Monigatti F, Dorff K, Campagne F, Bachur R, Steen H. Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin. Appl.3, 1052–1061 (2009).
   PubMed Web of Science ®Google Scholar
• Fang X, Balgley BM, Lee CS. Recent advances in capillary electrophoresis-based proteomic techniques for biomarker discovery. Electrophoresis30, 3998–4007 (2009).
   PubMed Web of Science ®Google Scholar
• Liu C-M. Clinical diagnosis by CE. In: Encyclopedia of Chromatography (3rd Edition). Cazes J (Ed.). CRC Press, FL, USA, 1, 449–453 (2010).
   Google Scholar
• Mischak H, Coon JJ, Novak J, Weissinger EM, Schanstra JP, Dominiczak AF. Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments. Mass Spectrom. Rev.28, 703–724 (2009).
   PubMed Web of Science ®Google Scholar
• Zuerbig P, Schiffer E, Mischak H. Capillary electrophoresis coupled to mass spectrometry for urinary proteome analysis. In: Renal and Urinary Proteomics: Methods and Protocols. Thongboonkerd V (Ed.). Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 321–332 (2010).
   Google Scholar
• Metzger J, Luppa PB, Good DM, Mischak H. Adapting mass spectrometry-based platforms for clinical proteomics applications: the capillary electrophoresis coupled mass spectrometry paradigm. Crit. Rev. Clin. Lab. Sci.46, 129–152 (2009).
   PubMed Web of Science ®Google Scholar
• Castagna A, Cecconi D, Boschetti E, Righetti PG. Prefractionation of urinary proteins. In: Renal and Urinary Proteomics: Methods and Protocols. Thongboonkerd V (Ed.). Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 201–217 (2010).
   Google Scholar
• Pragst F, Maurer HH, Hallbach J et al. Screening procedures for ‘general unknown’ analysis. Clinical Toxicological Analysis. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 1, 107–187 (2009).
   Google Scholar
• Stoll DR. Recent progress in online, comprehensive two-dimensional high-performance liquid chromatography for non-proteomic applications. Anal. Bioanal. Chem.397, 979–986 (2010).
   PubMed Web of Science ®Google Scholar
• Bazzi C. IgA nephropathy: clinical significance of urinary proteins/polypeptides characterization. Curr. Proteomics6, 179–186 (2009).
   Google Scholar
• Deyarajan P, Ross GF. Surface-enhanced laser desorption/ionization for urinary proteome analysis. In: Renal and Urinary Proteomics: Methods and Protocols. Thongboonkerd V (Ed.). Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 299–320 (2010).
   Google Scholar
• Liu B-C, Lv L-L, Zhang L. Antibody microarrays for urinary proteome profiling. In: Renal and Urinary Proteomics. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 349–366 (2010).
   Google Scholar
• Marouga R, David S, Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem.382(3), 669–678. (2005).
   PubMed Web of Science ®Google Scholar
• Candiano G, Santucci L, Petretto A et al. 2D-electrophoresis and the urine proteome map: where do we stand? J. Proteomics73, 829–844 (2010).
   PubMed Web of Science ®Google Scholar
• Ramachandra RSP, Shaw MA, Sharma K. 2-D difference in-gel electrophoresis (2-D DIGE) and urinary proteomics.In: Renal and Urinary Proteomics: Methods and Protocols. Thongboonkerd V (Ed.). Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 253–269 (2010).
   Google Scholar
• Silva JC, Denny R, Dorschel CA et al. Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem.77(7), 2187–2200 (2005).
   PubMed Web of Science ®Google Scholar
• Silva JC, Gorenstein MV, Li G-Z, Vissers JPC, Geromanos SJ. Absolute quantification of proteins by LCMSE. Mol. Cell Proteomics5, 144–156 (2006).
   PubMed Web of Science ®Google Scholar
• Chandrakumaran A, Hortebusch Z, König S. Urine profiling using ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry and pattern analysis. Biomacromolecular Mass Spectr.2(3), 199–210 (2010).
   Google Scholar
• Gika HG, Theodoridis GA, Earll M, Snyder RW, Sumner SJ, Wilson ID. Does the mass spectrometer define the marker? A comparison of global metabolite profiling data generated simultaneously via UPLC–MS on two different mass spectrometers. Anal. Chem.82(19), 8226–8234 (2010).
   Google Scholar
• Coppens A, Speeckaert M, Delanghe J. The pre-analytical challenges of routine urinalysis. Acta Clin. Belg.65, 182–189 (2010).
   PubMed Web of Science ®Google Scholar
• Lauridsen M, Hansen SH, Jaroszewski JW, Cornett C. Human urine as test material in 1H NMR-based metabonomics: recommendations for sample preparation and storage. Anal. Chem.79, 1181–1186 (2007).
   PubMed Web of Science ®Google Scholar
• Gika H, Theodoritis GA, Wilson ID. 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. A1189(1–2), 314–322 (2008).
   PubMed Web of Science ®Google Scholar
• Want EJ, Wilson ID, Gika H et al. Global metabolic profiling procedures for urine using UPLC–MS. Nat. Protoc.5, 1005–1018 (2010).
   PubMed Web of Science ®Google Scholar
• Zhang XK, Dutky RC, Fales HM. Rubber stoppers as sources of contaminants in electrospray analysis of peptides and proteins. Anal. Chem.68(18), 3288–3289 (1996).
   PubMed Web of Science ®Google Scholar
• Biemann K. Mass Spectrometry, Organic Chemical Applications. McGraw-Hill Book Company, Inc., NY, USA (1962).
   Google Scholar
• Ji AJ, Jiang Z-P, Livson Y, Davis JA, Chu JX-G, Weng N-D. Challenges in urine bioanalytical assays: overcoming nonspecific binding. Bioanalysis2, 1573–1586 (2010).
   Google Scholar
• Alvarez-Sanchez B, Priego-Capote F, Luque de Castro MD. Metabolomics analysis I. Selection of biological samples and practical aspects preceding sample preparation. Trends Anal. Chem.29, 111–119 (2010).
   Web of Science ®Google Scholar
• Chiu ML, Lawi W, Snyder ST, Wong PK, Liao JC, Gau V. Matrix effects – a challenge toward automation of molecular analysis. JALA15, 233–242 (2010).
   Web of Science ®Google Scholar
• Thomas CE, Sexton W, Benson K, Sutphen R, Koomen J. Urine collection and processing for protein biomarker discovery and quantification. Cancer Epidemiol. Biomarkers Prev.19, 953–959 (2010).
   PubMed Web of Science ®Google Scholar
• Qiu Y, Cai G, Su M et al. Urinary metabonomic study on colorectal cancer. J. Proteome Res.9, 1627–1634 (2010).
   PubMed Web of Science ®Google Scholar
• Zhang Z, Qiu Y, Hua Y et al. Serum and Urinary metabonomic study of human osteosarcoma. J. Proteome Res.9, 4861–4868 (2010).
   Google Scholar
• Pasikanti KK, Esuvaranathan K, Ho PC et al. Noninvasive urinary metabonomic diagnosis of human bladder cancer. J. Proteome Res.9, 2988–2995 (2010).
   PubMed Web of Science ®Google Scholar
• Kim J-W, Lee G, Moon S-M et al. Metabolomic screening and star pattern recognition by urinary amino acid profile analysis from bladder cancer patients. Metabolomics6(2), 202–206 (2010).
   Web of Science ®Google Scholar
• Li X, Yang S, Qiu Y et al. Urinary metabolomics as a potentially novel diagnostic and stratification tool for knee osteoarthritis. Metabolomics6(1), 109–118 (2010).
   Google Scholar
• Lee J, Kim M-H, Ha M, Chung BC. Urinary metabolic profiling of volatile organic compounds in acute exposed volunteers after an oil spill in Republic of Korea. Biomed. Chromatogr.24(5), 562–568 (2010).
   Google Scholar
• Beckmann M, Enot DP, Overy DP et al. Metabolite fingerprinting of urine suggests breed-specific dietary metabolism differences in domestic dogs. Br. J. Nutr.103(8), 1127–1138 (2010).
   Google Scholar
• Taylor SL, Ganti S, Bukanov NO et al. A metabolomics approach using juvenile cystic mice to identify urinary biomarkers and altered pathways in polycystic kidney disease. Am. J. Physiol. Renal Physiol.298(4), F909–F922 (2010).
   PubMedGoogle Scholar
• Kouremenos KA, Pitt J, Marriott PJ. Metabolic profiling of infant urine using comprehensive two-dimensional gas chromatography: application to the diagnosis of organic acidurias and biomarker discovery. J. Chromatogr. A1217(1), 104–111 (2010).
   PubMedGoogle Scholar
• Kumar BS, Lee Y-J, Yi HJ, Chung BC, Jung BH. Discovery of safety biomarkers for atorvastatin in rat urine using mass spectrometry based metabolomics combined with global and targeted approach. Anal. Chim. Acta661(1), 47–59 (2010).
   PubMed Web of Science ®Google Scholar
• van Dorsten FA, Grün CH, van Velzen EJ, Jacobs DM, Draijer R, van Duynhoven JP. The metabolic fate of red wine and grape juice polyphenols in humans assessed by metabolomics. Mol. Nutr. Food Res.54, 897–908 (2010).
   PubMed Web of Science ®Google Scholar
• Nevedomskaya E, Ramautar R, Derks R et al. CE–MS for metabolic profiling of volume-limited urine samples: application to accelerated aging TTD mice. J. Proteome Res.9, 4869–4874 (2010).
   PubMedGoogle Scholar
• Wang W, Feng B, Li X et al. Urinary metabolic profiling of colorectal carcinoma based on online affinity solid phase extraction-high performance liquid chromatography and ultra performance liquid chromatography-mass spectrometry. Mol. Bio. Syst.6, 1947–1955 (2010).
   Google Scholar
• Wang P, Sun H, Lv H et al. Thyroxine and reserpine-induced changes in metabolic profiles of rat urine and the therapeutic effect of Liu Wei Di Huang Wan detected by UPLC–HDMS. J. Pharm. Biomed. Anal.53, 631–645 (2010).
   PubMed Web of Science ®Google Scholar
• Manna SK, Patterson AD, Yang Q et al. Identification of noninvasive biomarkers for alcohol-induced liver disease using urinary metabolomics and the Ppara-null mouse. J. Proteome Res.9, 4176–4188 (2010).
   PubMed Web of Science ®Google Scholar
• Legido-Quigley C, Stella C, Perez-Jimenez F et al. Liquid chromatography-mass spectrometry methods for urinary biomarker detection in metabonomic studies with application to nutritional studies. Biomed. Chromatogr.24(7), 737–743 (2010).
   Google Scholar
• Michopoulos F, Theodoridis G, Smith CJ, Wilson ID. Metabolite profiles from dried biofluid spots for metabonomic studies using UPLC combined with oaTOF–MS. J. Proteome Res.9, 3328–3334 (2010).
   PubMed Web of Science ®Google Scholar
• Zhao H, Fan M, Fan L, Sun J, Guo D. Liquid chromatography-tandem mass spectrometry analysis of metabolites in rats after administration of prenylflavonoids from Epimediums. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.878(15–16), 1113–1124 (2010).
   PubMed Web of Science ®Google Scholar
• Li Y, Liu S, Wang C et al. Novel biomarkers of 3-chloro-1,2-propanediol exposure by ultra performance liquid chromatography/mass spectrometry based metabonomic analysis of rat urine. Chem. Res. Toxicol.23, 1012–1017 (2010).
   PubMed Web of Science ®Google Scholar
• Zheng S, Yu M, Lu X et al. Urinary metabonomic study on biochemical changes in chronic unpredictable mild stress model of depression. Clin. Chim. Acta411(2–3), 204–209 (2010).
   PubMed Web of Science ®Google Scholar
• An Z, Chen Y, Zhang R et al. Integrated ionization approach for RRLC–MS/MS-based metabonomics, finding potential biomarkers for lung cancer. J. Proteome Res.9(8), 4071–4081 (2010).
   PubMed Web of Science ®Google Scholar
• Twohig M, Shockcor JP, Wilson ID, Nicholson JK, Plumb RS. Use of an atmospheric solids analysis probe (ASAP) for high throughput screening of biological fluids, preliminary applications on urine and bile. J. Proteome Res.9(7), 3590–3597 (2010).
   PubMed Web of Science ®Google Scholar
• Andersen S, Mischak H, Zurbig P, Parving H-H, Rossing P. Urinary proteome analysis enables assessment of renoprotective treatment in Type 2 diabetic patients with microalbuminuria. BMC Nephrol.11, 29 (2010).
   PubMed Web of Science ®Google Scholar
• Liang S-L, Clarke W. Urine proteomic profiling for biomarkers of acute renal transplant rejection. Methods Mol. Biol.641, 185–191 (2010).
   Google Scholar