Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome

Journal of Proteomics

Volumn 75, Issue 1, 2011, Pages 70-80

  Molina, Laurence ^a,d   Salvetat, Nicolas ^a,d   Ameur, Randa Ben ^a,d   Peres, Sabine ^a,d   Sommerer, Nicolas ^b   Jarraya, Fayçal ^c,d   Ayadi, Hammadi ^c,d   Molina, Franck ^a,d   Granier, Claude ^a,d  

^a U896 Inserm CRLC Val d'Aurelle   (France)

^b CEMAGREF   (France)

^c CENTRE DE BIOTECHNOLOGIE DE SFAX   (Tunisia)

^d L I A 135 Laboratoire International Associé CNRS   (France)

Author keywords

Normal urine; Proteome; Two dimensional gel electrophoresis; Variability

Indexed keywords

ALBUMIN; ALPHA 1 ANTITRYPSIN; ALPHA 1BETA BLYCOPROTEIN; ANTIBODY FRAGMENT; BASEMENT MEMBRANE SPECIFIC HEPARAN; CADHERIN; CD14 ANTIGEN; CELL ADHESION MOLECULE 4; GELSOLIN; GLUCAN 1,4 ALPHA GLUCOSIDASE; GLUTAMINYL PEPTIDE CYCLOTRANSFERASE; KININOGEN I; LYSOSOMAL ACID PHOSPHATASE; MANNAN BINDING LECTIN SERINE PROTEASE 2; PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN 4; PROSTAGLANDIN D2 SYNTHASE; PROTEIN; PROTEIN AMBP; PROTEOME; SEROTRANSFERRIN; SULFATE PROTEOGLYCAN CORE PROTEIN; TAMM HORSFALL GLYCOPROTEIN; TRYPSINOGEN 4; UNCLASSIFIED DRUG; ZINC ALPHA 2 GLYCOPROTEIN; MAJOR URINARY PROTEINS;

ADULT; ARTICLE; CLINICAL ARTICLE; FEMALE; HUMAN; MALE; MASS SPECTROMETRY; NORMAL HUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN URINE LEVEL; QUANTITATIVE ANALYSIS; STORAGE; TEMPERATURE; TWO DIMENSIONAL GEL ELECTROPHORESIS; URINALYSIS; CHEMISTRY; METHODOLOGY; MIDDLE AGED; REFERENCE VALUE; URINE;

ADULT; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FEMALE; HUMANS; MALE; MASS SPECTROMETRY; MIDDLE AGED; PROTEINS; PROTEOME; REFERENCE VALUES; URINE;

EID: 84858744962     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.06.031     Document Type: Article

References (48)

1. Decramer S., Gonzalez de Peuto A., Breuil B., et al. Urine in clinical proteomics. Mol Cell Proteomics 2008.
2. Lee R.S., Monigatti F., Briscoe A.C., Waldon Z., Freeman M.R., Steen H. Optimizing sample handling for urinary proteomics. J Proteome Res 2008, 7:4022-4030.
3. Anderson N.G., Anderson N.L., Tollaksen S.L. Proteins of human urine. I. Concentration and analysis by two-dimensional electrophoresis. Clin Chem 1979, 25:1199-1210.
4. Thongboonkerd V., Gozal E., Sachleben L.R., Arthur J.M., Pierce W.M., Cai J., et al. Proteomic analysis reveals alterations in the renal kallikrein pathway during hypoxia-induced hypertension. J Biol Chem 2002, 277:34708-34716.
5. Spahr C.S., Davis M.T., McGinley M.D., Robinson J.H., Bures E.J., Beierle J., et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 2001, 1:93-107.
6. Schaub S., Wilkins J., Weiler T., Sangster K., Rush D., Nickerson P. Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int 2004, 65:323-332.
7. Sun W., Li F., Wu S., Wang X., Zheng D., Wang J., et al. Human urine proteome analysis by three separation approaches. Proteomics 2005, 5:4994-5001.
8. Pisitkun T., Shen R.F., Knepper M.A. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci USA 2004, 101:13368-13373.
9. Pieper R., Gatlin C.L., McGrath A.M., Makusky A.J., Mondal M., Seonarain M., et al. 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.
10. Castagna A., Cecconi D., Sennels L., Rappsilber J., Guerrier L., Fortis F., et al. Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res 2005, 4:1917-1930.
11. Soldi M., Sarto C., Valsecchi C., Magni F., Proserpio V., Ticozzi D., et al. Proteome profile of human urine with two-dimensional liquid phase fractionation. Proteomics 2005, 5:2641-2647.
12. Oh J., Pyo J.H., Jo E.H., Hwang S.I., Kang S.C., Jung J.H., et al. Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 2004, 4:3485-3497.
13. Zerefos P.G., Vougas K., Dimitraki P., Kossida S., Petrolekas A., Stravodimos K., et al. Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE. Proteomics 2006, 6:4346-4355.
14. Wang L., Li F., Sun W., Wu S., Wang X., Zhang L., et al. Concanavalin A-captured glycoproteins in healthy human urine. Mol Cell Proteomics 2006, 5:560-562.
15. Sleat D.E., Zheng H., Lobel P. The human urine mannose 6-phosphate glycoproteome. Biochim Biophys Acta 2007, 1774:368-372.
16. Ru Q.C., Katenhusen R.A., Zhu L.A., Silberman J., Yang S., Orchard T.J., et al. Proteomic profiling of human urine using multi-dimensional protein identification technology. J Chromatogr A 2006, 1111:166-174.
17. Khan A., Packer N.H. Simple urinary sample preparation for proteomic analysis. J Proteome Res 2006, 5:2824-2838.
18. Adachi J., Kumar C., Zhang Y., Olsen J.V., Mann M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol 2006, 7:R80.
19. Candiano G., Santucci L., Petretto A., Bruschi M., Dimuccio V., Urbani A., et al. 2D-electrophoresis and the urine proteome map: where do we stand?. J Proteomics 2010, 73:829-844.
20. Nagaraj N., Mann M. Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome. J Proteome Res 2011, 10:637-645.
21. Thongboonkerd V., Chutipongtanate S., Kanlaya R. Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J Proteome Res 2006, 5:183-191.
22. Lafitte D., Dussol B., Andersen S., Vazi A., Dupuy P., Jensen O.N., et al. Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples. Clin Biochem 2002, 35:581-589.
23. Thongboonkerd V. Practical points in urinary proteomics. J Proteome Res 2007, 6:3881-3890.
24. Weekes J., Wheeler C.H., Yan J.X., Weil J., Eschenhagen T., Scholtysik G., et al. Bovine dilated cardiomyopathy: proteomic analysis of an animal model of human dilated cardiomyopathy. Electrophoresis 1999, 20:898-906.
25. Molina L., Grimaldi M., Robert-Hebmann V., Espert L., Varbanov M., Devaux C., et al. Proteomic analysis of the cellular responses induced in uninfected immune cells by cell-expressed X4 HIV-1 envelope. Proteomics 2007, 7:3116-3130.
26. Copois V., Bibeau F., Bascoul-Mollevi C., Salvetat N., Chalbos P., Bareil C., et al. Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J Biotechnol 2007, 127:549-559.
27. Peres S., Molina L., Salvetat N., Granier C., Molina F. A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics. BMC Bioinformatics 2008, 9:460.
28. Li S.J., Peng M., Li H., Liu B.S., Wang C., Wu J.R., et al. Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res 2009, 37:D907-D912.
29. Smith G., Barratt D., Rowlinson R., Nickson J., Tonge R. Development of a high-throughput method for preparing human urine for two-dimensional electrophoresis. Proteomics 2005, 5:2315-2318.
30. 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.
31. Sharma K., Lee S., Han S., Lee S., Francos B., McCue P., et al. Two-dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy. Proteomics 2005, 5:2648-2655.
32. O'Riordan E., Orlova T.N., Mei J.J., Butt K., Chander P.M., Rahman S., et al. Bioinformatic analysis of the urine proteome of acute allograft rejection. J Am Soc Nephrol 2004, 15:3240-3248.
33. Traum A.Z., Wells M.P., Aivado M., Libermann T.A., Ramoni M.F., Schachter A.D. SELDI-TOF MS of quadruplicate urine and serum samples to evaluate changes related to storage conditions. Proteomics 2006, 6:1676-1680.
34. Theodorescu D., Wittke S., Ross M.M., Walden M., Conaway M., Just I., et al. Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol 2006, 7:230-240.
35. Fiedler G.M., Baumann S., Leichtle A., Oltmann A., Kase J., Thiery J., et al. Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin Chem 2007, 53:421-428.
36. Havanapan P.O., Thongboonkerd V. Are protease inhibitors required for gel-based proteomics of kidney and urine?. J Proteome Res 2009, 8:3109-3117.
37. Afkarian M., Bhasin M., Dillon S.T., Guerrero M.C., Nelson R.G., Knowler W.C., et al. Optimizing a proteomics platform for urine biomarker discovery. Mol Cell Proteomics 2010, 9:2195-2204.
38. Coon J.J., Zurbig P., Dakna M., Dominiczak A.F., Decramer S., Fliser D., et al. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clin Appl 2008, 2:964.
39. Gorg A., Weiss W., Dunn M.J. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004, 4:3665-3685.
40. Hortin G.L., Sviridov D. Diagnostic potential for urinary proteomics. Pharmacogenomics 2007, 8:237-255.
41. Thongboonkerd V., Malasit P. Renal and urinary proteomics: current applications and challenges. Proteomics 2005, 5:1033-1042.
42. Tryggvason K., Pettersson E. Causes and consequences of proteinuria: the kidney filtration barrier and progressive renal failure. J Intern Med 2003, 254:216-224.
43. Blouch K., Deen W.M., Fauvel J.P., Bialek J., Derby G., Myers B.D. Molecular configuration and glomerular size selectivity in healthy and nephrotic humans. Am J Physiol 1997, 273:F430-F437.
44. Oesterling J.E., Jacobsen S.J., Chute C.G., Guess H.A., Girman C.J., Panser L.A., et al. Serum prostate-specific antigen in a community-based population of healthy men. Establishment of age-specific reference ranges. JAMA 1993, 270:860-864.
45. Breul J., Pickl U., Hartung R. Prostate-specific antigen in urine. Eur Urol 1994, 26:18-21.
46. Breul J., Pickl U., Schaff J. Extraprostatic production of prostate specific antigen is under hormonal control. J Urol 1997, 157:212-213.
47. Mannello F., Condemi L., Cardinali A., Bianchi G., Gazzanelli G. High concentrations of prostate-specific antigen in urine of women receiving oral contraceptives. Clin Chem 1998, 44:181-183.
48. Anderson N.L., Anderson N.G., Haines L.R., Hardie D.B., Olafson R.W., Pearson T.W. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 2004, 3:235-244.