Analysis of the urine proteome via a combination of multi-dimensional approaches

Proteomics

Volumn 12, Issue 3, 2012, Pages 391-400

  Zerefos, Panagiotis G ^a   Aivaliotis, Michalis ^a,c   Baumann, Marc ^b   Vlahou, Antonia ^a  

^a Division of Biotechnology   (Greece)

^b BIOMEDICUM HELSINKI   (Finland)

^c INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

Author keywords

Electrophoresis; LC MS MS; Multi dimensional separation; Technology; Urine

Indexed keywords

PROTEOME;

ARTICLE; CONTROLLED STUDY; GEL ELECTROPHORESIS; HUMAN; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MALE; MASS SPECTROMETRY; METHODOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN URINE LEVEL; URINALYSIS;

CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; MALE; PEPTIDES; PROTEIN ISOFORMS; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; URINE;

EID: 84856479041     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100212     Document Type: Article

References (31)

1. Good, D. M., Thongboonkerd, V., Novak, J., Bascands, J. L. et al., Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J. Proteome Res. 2007, 6, 4549-4555.
2. Thongboonkerd, V., Current status of renal and urinary proteomics: ready for routine clinical application? Nephrol. Dial. Transplant. 2010, 25, 11-16.
3. Good, D. M., Zurbig, P., Argiles, A., Bauer, H. W. et al., Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol. Cell. Proteomics 2010, 9, 2424-2437.
4. Oh, J., Pyo, J. H., Jo, E. H., Hwang, S. I. et al., Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 2004, 4, 3485-3497.
5. Park, M. R., Wang, E. H., Jin, D. C., Cha, J. H. et al., Establishment of a 2-D human urinary proteomic map in IgA nephropathy. Proteomics 2006, 6, 1066-1076.
6. Zerefos, P. G., Vougas, K., Dimitraki, P., Kossida, S. et al., Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE. Proteomics 2006, 6, 4346-4355.
7. 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.
8. Davis, M. T., Spahr, C. S., McGinley, M. D., Robinson, J. H. et al., Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. II. Limitations of complex mixture analyses. Proteomics 2001, 1, 108-117.
9. Moon, M. H., Myung, S., Plasencia, M., Hilderbrand, A. E., Clemmer, D. E., Nanoflow LC/ion mobility/CID/TOF for proteomics: Analysis of a human urinary proteome. J. Proteome Res. 2003, 2, 589-597.
10. Soldi, M., Sarto, C., Valsecchi, C., Magni, F. et al., Proteome profile of human urine with two-dimensional liquid phase fractionation. Proteomics 2005, 5, 2641-2647.
11. Schaub, S., Wilkins, J., Weiler, T., Sangster, K. et al., Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int. 2004, 65, 323-332.
12. Cadieux, P. A., Beiko, D. T., Watterson, J. D., Burton, J. P. et al., Surface-enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS): a new proteomic urinary test for patients with urolithiasis. J. Clin. Lab. Anal. 2004, 18, 170-175.
13. Siwy, J., Mullen, W., Golovko, I., Franke, J., Zürbig, P., Human urinary peptide database for multiple disease biomarker discovery. Proteomics Clin. Appl. 2011, 5, 367-374.
14. 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.
15. Pieper, R., Gatlin, C. L., McGrath, A. M., Makusky, A. J. 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.
16. 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.
17. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J. et al., Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res. 2005, 4, 1917-1930.
18. Kentsis, A., Monigatti, F., Dorff, K., Campagne, F. et al., Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin. Appl. 2009, 3, 1052-1061.
19. Candiano, G., Santucci, L., Petretto, A., Bruschi, M. et al., 2D-electrophoresis and the urine proteome map: Where do we stand? J. Proteomics 2010, 73, 829-844.
20. Mischak, H., Kolch, W., Aivaliotis, M., Bouyssie, D. et al., Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics Clin. Appl. 2010, 4, 464-478.
21. Keller, A., Nesvizhskii, A. I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383-5392.
22. Theodorescu, D., Wittke, S., Ross, M. M., Walden, M. et al., Discovery and validation of new protein biomarkers for urothelial cancer: A prospective analysis. Lancet Oncol. 2006, 7, 230-240.
23. Fountoulakis, M., Juranville, J. F., Roder, D., Evers, S. et al., Reference map of the low molecular mass proteins of Haemophilus influenzae. Electrophoresis 1998, 19, 1819-1827.
24. Fountoulakis, M., Dimitraki, P., Protein fractionation by preparative electrophoresis. Methods Mol. Biol. 2008, 424, 301-313.
25. Fountoulakis, M., Juranville, J. F., Tsangaris, G., Suter, L., Fractionation of liver proteins by preparative electrophoresis. Amino Acids 2004, 26, 27-36.
26. Michalski, A., Cox, J., Mann, M., More than 100000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J. Proteome Res. 2011, 10, 1785-1793.
27. Duncan, M. W., Aebersold, R., Caprioli, R. M., The pros and cons of peptide-centric proteomics. Nat. Biotechnol. 2010, 28, 659-664.
28. Eisenacher, M., Schnabel, A., Stephan, C., Quality meets quantity - quality control, data standards and repositories. Proteomics 2011, 11, 1031-1036.
29. Eisenacher, M., Martens, L., Hardt, T., Kohl, M. et al., Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics 2009, 9, 3928-3933.
30. Hermjakob, H., Apweiler, R., The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: Making proteomics data accessible. Expert Rev. Proteomics 2006, 3, 1-3.
31. Mischak, H., Allmaier, G., Apweiler, R., Attwood, T. et al., Recommendations for biomarker identification and qualification in clinical proteomics. Sci. Transl. Med. 2010, 2, 42-46.