Simple urinary sample preparation for proteomic analysis

Journal of Proteome Research

Volumn 5, Issue 10, 2006, Pages 2824-2838

  Khan, Alamgir ^a   Packer, Nicolle H ^b  

^a MACQUARIE UNIVERSITY   (Australia)

^b Proteome Systems Ltd   (Australia)

Author keywords

2 D gel electrophoresis; MALDI TOF; Ovarian cancer; Precipitation; Urinary proteome; Urine

Indexed keywords

ACETONITRILE; PROTEOME;

ARTICLE; CONCENTRATION (PARAMETERS); DESALINATION; GENE MAPPING; GENE SEQUENCE; HUMAN; MOLECULAR WEIGHT; NUCLEOTIDE SEQUENCE; OVARY CANCER; PLASMA; PRECIPITATION; PRIORITY JOURNAL; PROTEOMICS; TWO DIMENSIONAL ELECTROPHORESIS; UNINDEXED SEQUENCE; URINALYSIS;

ADULT; FEMALE; HUMANS; HYDROGEN-ION CONCENTRATION; MALE; NEOPLASM PROTEINS; OVARIAN NEOPLASMS; PROTEINS; PROTEOME; PROTEOMICS; URINE;

EID: 33750131662     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr060305y     Document Type: Article

References (40)

1. Anderson, N. G.; Anderson, N. L.; Tollaksen, S. L.; Hahn, H.; Giere, F.; Edwards, J. Concentration and two-dimensional electrophoretic analysis of human urinary proteins. Anal. Biochem. 1979, 95, 48-61.
2. Vlahou, A.; Schellhammer, P. F.; Mendrinos, S.; Patel, K.; Kondylis, F. I.; Gong, L.; Nasim, S.; Wright, G. L., Jr. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am. J. Pathol. 2001, 158, 1491-1502.
3. Pang, J. X.; Ginanni, N.; Dongre, A. R.; Hefta, S. A.; Opitek, G. J. Biomarker discovery in urine by proteomics. J. Proteome Res. 2002, 1, 161-169.
4. Bratt, O. Hereditary prostate cancer: clinical aspects. J. Urol. 2002, 168, 906-913.
5. Breul, J.; Pickl, U.; Hartung, R. Prostate-specific antigen in urine. Eur. Urol. 1994, 26, 18-21.
6. Jellum, E.; Dollekamp, H.; Blessum, C. Capillary electrophoresis for clinical problem solving: Analysis of urinary diagnostic metabolites and serum proteins. J. Chromatogr., B. 1998, 683, 55-65.
7. Cutler, P.; Bell, D. J.; Birrell, H. C.; Connelly, J. C.; Connor, S. C.; Holmes, E.; Mitchell, B. C.; Monte, S. Y.; Neville, B. A.; Pickford, R.; Polley, S.; Schneider, K.; Skehel, J. M. An integrated proteomic approach to studying glomerular nephrotoxicity. Electrophoresis 1999, 20, 3647-3658.
8. Aviles-Santa, L.; Alpern, R.; Raskin, P. Reversible acute renal failure and nephrotic syndrome in a Type 1 diabetic patient. J. Diabetes Complications 2002, 16, 249-254.
9. Svensson, M.; Sundkvist, G.; Arnqvist, H. J.; Bjork, E.; Blohme, G.; Bolinder, J.; Henricsson, M.; Nystrom, L.; Torffvit, O.; Waernbaum, I.; Ostman, J.; Eriksson, J. W. Signs of nephropathy may occur early in young adults with diabetes despite modern diabetes management. Diabetes Care 2003, 26, 2903-2909.
10. Kennedy, S. Proteomic profiling from human samples: the body fluid alternative. Toxicol. Lett. 2001, 120, 379-384.
11. Khan, A.; Grinyer, J.; Truong, S. T.; Breen, E. J.; Packer, N. H. New urinary EPO drug testing method using two-dimensional gel electrophoresis. Clin. Chim. Acta 2005, 358, 119-130.
12. Kiernan, U. A.; Tubbs, K. A.; Nedelkov, D.; Niederkofler, E. E.; McConnell, E.; Nelson, R. W. Comparative urine protein phenotyping using mass spectrometric immunoassay. J. Proteome Res. 2003, 2, 191-197.
13. Lafitte, D.; Dussol, B.; Andersen, S.; Vazi, A.; Dupuy, P.; Jensen, O. N.; Berland, Y.; Verdier, J. M. Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples. Clin. Biochem. 2002, 35, 581-589.
14. Rehman, I.; Azzouzi, A. R.; Catto, J. W.; Allen, S.; Cross, S. S.; Feeley, K.; Meuth, M.; Hamdy, F. C. Proteomic analysis of voided urine after prostatic massage from patients with prostate cancer: a pilot study. Urology 2004, 64, 1238-1243.
15. Marshall, T.; Williams, K. M. Clinical analysis of human urinary proteins using high-resolution electrophoretic methods. Electrophoresis 1998, 19, 1752-1770.
16. Ferslew, K. E.; Hagardorn, A. N.; Robert, T. A. Capillary ion electrophoresis of endogenous anions and anionic adulterants in human urine. J. Forensic Sci. 2001, 46, 615-626.
17. Rasmussen, H. H.; Orntoft, T. F.; Wolf, H.; Celis, J. E. Towards a comprehensive database of proteins from the urine of patients with bladder cancer. J. Urol. 1996, 155, 2113-2119.
18. Tantipaiboonwong, P.; Sinchaikul, S.; Sriyam, S.; Phutrakul, S.; Chen, S. T. Different techniques for urinary protein analysis of normal and lung cancer patients. Proteomics 2005, 5, 1140-1149.
19. Thongboonkerd, V.; McLeish, K. R.; Arthur, J. M.; Klein, J. B. Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int. 2002, 62, 1461-1469.
20. Emslie, K. R.; Howe, C.; Trout, G. Measurement of urinary erythropoietin levels in athletes. In Recent Advances in Doping Analysis (7), Proceedings of the Manfred Donike Workshop, 17th Cologne Workshop on Dope Analysis; Schänzer, W., Geyer, H., Gotzmann, A., Mareck-Engelke, U., Eds.; Sport & Buch Strauss: Cologne, Germany, 1999; pp 291-299.
21. Azevedo, H.; Bishop, D.; Cavaco-Paulo, A. Possibilities for recycling cellulases after use in cotton processing: part II: Separation of cellulases from reaction products and released dyestuffs by Ultrafiltration. Appl. Biochem. Biotech. 2002, 101, 77-91.
22. Glee, P. M.; Masuoka, J.; Ozier, W. T.; Hazen, K. C. Presence of multiple laminin- and fibronectin-binding proteins in cell wall extract of Candida albicans: influence of dialysis. J. Med. Vet. Mycol. 1998, 34, 57-61.
23. Meyer, T. H.; Bohler, J.; Frahm, A. W. Determination of Cremophor EL in plasma after sample preparation with solid-phase extraction and plasma protein precipitation. J. Pharm. Biomed. Anal. 2001, 24, 495-506.
24. Samanidou, V. F.; Demetriou, C. E.; Papadoyannis, I. N. Direct determination of four fluoroquinolones, enoxacin, norfloxacin, ofloxacin, and ciprofloxacin, in pharmaceuticals and blood serum by HPLC. Anal. Bioanal. Chem. 2003, 375, 623-629.
25. Celis, J. E.; Rasmussen, H. H.; Vorum, H.; Madsen, P.; Honore, B.; Wolf, H.; Orntoft, T. F. Bladder squamous cell carcinomas express psoriasin and externalize it to the urine. J. Urol. 1996, 155, 2105-2112.
26. Hansen, H. P.; Hovind, P.; Jensen, B. R.; Parving H. H. Diurnal variations of glomerular filtration rate and albuminuria in diabetic nephropathy. Kidney Int. 2002, 61, 163-168.
27. Banks, R. E.; Porter, W. H.; Whelan, P.; Smith, P. H.; Selby, P. J. Soluble forms of the adhesion molecule E-cadherin in urine. J. Clin. Pathol. 1995, 48, 179-180.
28. Spahr, C. S.; Davis, M. T.; McGinley, M. D.; Robinson, J. H.; Bures, E. J.; Beierle, J.; Mort, J.; Courchesne, P. L.; Chen, K.; Wahl, R. C.; Yu, W.; Luethy, R.; Patterson, S. D. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 2001, 1, 93-107.
29. Pieper, R.; Gatlin, C. L.; McGrath, A. M.; Makusky, A. J.; Mondal, M.; Seonarain, M.; Field, E.; Schatz, C. R.; Estock, M. A.; Ahmed, N.; Anderson, N. G.; Steiner, S. Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004, 4, 1159-1174.
30. Oh, J.; Pyo, J. H.; Jo, E. H.; Hwang, S. I.; Kang, S. C.; Jung, J. H.; Park, E. K.; Kim, S. Y.; Choi, J. Y.; Lim, J. Establishment of a near standard two-dimensional human urine proteomic map. Proteomics 2004, 4, 3485-4397.
31. Nabi, G.; N'Dow, J.; Hasan, T. S.; Booth, I. R.; Cash, P. Proteomic analysis of urine in patients with intestinal segments transposed into the urinary tract. Proteomics 2005, 5, 1729-1733.
32. Rasmussen, H. H.; Van Damme, J.; Bauw, G.; Puype, M.; Cells, J. E.; Vandekerckhove, J. In Methods in Protein Sequence Analysis; Jörnvall, H., Höög, J.-O., Gustavsson, A.-M., Eds.; Birkhäuser: Basel, Switzerland, 1991; pp 103-104.
33. Nielsen, M. L.; Bennett, K. L.; Larsen, B.; Moniatte, M.; Mann, M. Peptide end sequencing by orthogonal MALDI tandem mass spectrometry. J. Proteome Res. 2002, 1, 63-71.
34. Herbert, B.; Galvani, M.; Hamdan, M.; Olivieri, E.; MacCarthy, J.; Pedersen, S.; Righetti, P. G. Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how? Electrophoresis 2001, 22, 2046-2057.
35. Smejkal, G. B.; Lazarev, A.; Khan, A.; Robinson, M. H.; Theriault, S. E.; McCarthy, J. T. Development of new colloidal stains: narrowing the gap between coomassie and silver staining sensitivity. Presented at HUPO 2nd Annual & IUBMB XIX Joint World Congress, Montreal, Canada, 2003, October 8-11; poster presentation.
36. Wilson, N. L.; Schulz, B. L.; Karlsson, N. G.; Packer, N. H. Sequential analysis of N- and O-linked glycosylation of 2D-PAGE separated glycoproteins. J. Proteome Res. 2002, 1, 521-529.
37. Smejkal, G. B.; Li, C.; Robinson, M. H.; Lazarev, A. V.; Lawrence, N. P.; Chernokalskaya, E. Simultaneous reduction and alkylation of protein disulfides in a centrifugal ultrafiltration device prior to two-dimensional gel electrophoresis. J. Proteome Res. 2006, 5, 983-987.
38. Zhou, S.; Bailey, M. J.; Dunn, M. J.; Preedy, V. R.; Emery, P. W. A quantitative investigation into the losses of proteins at different stages of a two-dimensional gel electrophoresis procedure. Proteomics 2005, 5, 2739-2747.
39. Castagna, A.; Cecconi, D.; Sennels, L.; Rappsilber, J.; Guerrier, L.; Fortis, F.; Boschetti, E.; Lomas, L.; Righetti, P. G. Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res. 2005 4, 1917-1930.
40. Wilkins, M. R.; Appel, R. D.; Van Eyk, J. E.; Chung, M. C.; Gorg, A.; Hecker, M.; Huber, L. A.; Langen, H.; Link, A. J.; Paik, Y. K.; Patterson, S. D.; Pennington, S. R.; Rabilloud, T.; Simpson, R. J.; Weiss, W.; Dunn, M. J. Guidelines for the next 10 years of proteomics. Proteomics 2006 6, 4-8.