Surface-Enhanced Laser Desorption/Ionization for Urinary Proteome Analysis

Renal and Urinary Proteomics: Methods and Protocols

Volumn , Issue , 2009, Pages 299-320

  Devarajan, Prasad ^a   Ross, Gary F ^b  

^a CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^b BIO RAD LABORATORIES   (United States)

Author keywords

Binding buffers; Biomarkers; Immunoglobulins; Isoelectric point; Laser pulses; SELDI

Indexed keywords

EID: 79955773679     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527628612.ch23     Document Type: Chapter

References (55)

1. Zerhouni, E. (2003) The NIH Roadmap. Science, 302, 63-65.
2. Hutchens, T.W. and Yip, T.T. (1993) New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun Mass Spectrom, 7, 576-580.
3. Yip, T.T. and Lomas, L. (2002) SELDI ProteinChip array in oncoproteomic research. Technol Cancer Res Treat, 1 (4), 273-280.
4. Wadsworth, J.T., Somers, K.D., Cazares, L.H., Malik, G., Adam, B.L., Stack, B.C., Wright, G.L., and Semmes, O.J. (2004) Serum protein profiles to identify head and neck cancers. Clin Cancer Res, 10, 1625-1632.
5. Wilson, L.L., Tran, L., Morton, D.L., and Hoon, D.S. (2004) Detection of differentially expressed proteins in early-stage melanoma patients using SELDI-TOF mass spectrometry. Ann N Y Acad Sci, 1022, 317-322.
6. Zhang, Z., Bast, R.C. Jr, Yu, Y., Li, J., Sokoll, L.J., Rai, A.J., Rosenzweig, F.M., Cameron, B., Wang, Y.Y., Meng, X.Y., Berchuck, A., van Haaften-Day, C., Hacker, N.F., de Bruijn, H.W.A., van der Zee, H.J.A., Jacobs, I.J., Fung, E.T., and Chan, D.W. (2004) Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res, 64, 5882-5890.
7. Semmes, O.J., Feng, Z., Adam, B.L., Banez, L.L., Bigbee, W.L., Campos, D., Cazeras, L., Chan, D.W., Grizzle, W.E., Izbicka, E., Kagan, J., Malik, G., McLarren, D., Moul, J.W., Partin, A., Prasanna, P., Rosenzweig, J., Sokoll, L.J., Srivastava, S., Thompson, I., Welsh, M.J., White, N., Winget, M., Yasul, Y., Zhang, Z., and Zhu, L. (2005) Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate caner: I. Assessment of platform reproducibility. Clin Chem, 51, 102-112.
8. Fung, E.T., Yip, T.T., Lomas, L., Wang, Z., Yip, C., Meng, X.Y., Lin, S., Zhang, F., Zhang, Z., Chan, D.W., and Weinberger, S.R. (2005) Classification of cancer types by measuring variants of host response proteins using SELDI serum assays. Int J Cancer, 115, 783-789.
9. Clarke, C.H., Buckley, J.A., and Fung, E. (2005) SELDI-TOF-MS proteomics of breast cancer. Clin Chem Lab Med, 43, 1314-1320.
10. Li, J., Orland, R., White, C.N., Rosenzweig, J., Zhao, J., Seregni, E., Morelli, D., Yu, Y., Meng, X.Y., Zhang, Z., Davidson, N.E., Fung, E.T., and Chan, D.W. (2005) Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin Chem, 51, 2229-2235.
11. Beher, D., Wrigley, J., Owens, A.P., and Shearman, M.S. (2002) Generation of C-terminally truncated amyloid-beta peptides is dependent on gamma-secretase activity. J Neurochem, 82, 563-575.
12. Carrette, O., Demalte, I., Scherl, A., Yalkinoglu, O., Corthals, G., Burkhard, P., Hochstrasser, D.F., and Sanchez, J.C. (2003) A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease. Proteomics, 3, 1486-1494.
13. Furuta, M., Shiraishi, T., Okamoto, H., Mineta, T., Tabuchi, K., and Shiwa, M. (2004) Identification of pleiotrophin in conditioned medium secreted from neural stem cells. Dev Brain Res, 152, 189-197.
14. Chu, R., Zhang, W., Lim, H., Yeldandi, A.V., Herring, C., Brumfield, L., Reddy, J.K., and Davison, M. (2002) Profiling of acyl-CoA oxidase-deficient and peroxisome proliferator Wy14, 643-treated mouse liver. Gene Expr, 10, 165-177.
15. Dare, T.O., Davies, H.A., Turton, J.A., Lomas, L., Williams, T.C., and York, M.J. (2002) SELDI detection and identification of urinary parvalbumin-alpha. Electrophoresis, 23, 3241-3251.
16. Yuan, M. and Carmichael, W.W. (2004) Detection and analysis of the cyanobacterial peptide hepatotoxins microcystin and nodularin. Toxicon, 44, 561-570.
17. Vermeulen, R., Lan, Q., Zhang, L., Gunn, L., McCarthy, D., Woodbury, R.L., McGuire, M., Podust, V.N., Li, G., Chatterjee, N., Mu, R., Yin, S., Rothman, N., and Smith, M.T. (2005) Decreased levels of CXC-chemokines in serum of benzene-exposed workers identified by array-based proteomics. Proc Natl Acad Sci U S A, 102, 17041-17046.
18. Papadopoulos, M.C., Abel, P.M., Agranoff, D., Stich, A., Tarelli, E., Bell, B.A., Planche, T., Loosemore, A., Saadoun, S., Wilkins, P., and Krishna, S. (2004) A novel and accurate diagnostic test for human African trypanosomiasis. Lancet, 363, 1358-1363.
19. Gravett, M.G., Novy, M.J., Rosenfeld, R.G., Reddy, A.P., Jacob, T., Turner, M., McCormack, A., Lapidus, J.A., Hitti, J., Eschenbach, D.A., Roberts, C.T., and Nagalla, S.R. (2004) Diagnosis of intra-amniotic infection by proteomic profiling and identification of novel biomarkers. J Korean Am Med Assoc, 292, 462-469.
20. Kang, X., Xu, Y., Wu, X., Liang, Y., Wang, C., Guo, J., Wang, Y., Chen, M., Wu, D., Wang, Y., Bi, S., Qiu, Y., Lu, P., Cheng, J., Xiao, B., Hu, L., Gao, X., Liu, J., Wang, Y., Song, Y., Zhang, L., Suo, F., Chen, T., Huang, Z., Zhao, Y., Lu, H., Pan, C., and Tang, H. (2005) Proteomic fingerprints for potential application to early diagnosis of severe acute respiratory syndrome. Clin Chem, 51, 56-64.
21. Buhimschi, I.A., Christner, R., and Buhimschi, C.S. (2005) Proteomic biomarker analysis of amniotic fluid for identification of intra-amniotic inflammation. Br J Obstet Gynaecol, 112, 173-181.
22. Schaub, S., Wilkins, J., Weiler, T., Sangster, K., Rush, D., and Nickerson, P. (2004) Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int, 65, 323-332.
23. Nguyen, M., Ross, G., Dent, C., and Devarajan, P. (2005) Early prediction of acute renal injury using urinary proteomics. Am J Nephrol, 25, 318-326.
24. Thongboonkerd, V. (2004) Proteomics in nephrology: current status and future directions. Am J Nephrol, 24, 360-378.
25. Thongboonkerd, V. (2005) Proteomic analysis of renal diseases: unraveling the pathophysiology and biomarker discovery. Expert Rev Proteomics, 2, 349-366.
26. Vidal, B.C., Bonventre, J.V., and Hsu, S.I.-H. (2005) Towards the application of proteomics in renal disease diagnosis. Clin Sci, 109, 421-430.
27. Pisitkun, T., Johnstone, R., and Knepper, M.A. (2006) Discovery of urinary biomarkers. Mol Cell Proteomics, 5, 1760-1771.
28. O'Riordan, E., Gross, S.S., and Goligorsky, M.S. (2006) Technology insight: renal proteomics - at the crossroads between promise and problems. Nat Clin Pract Nephrol, 2, 445-458.
29. Schaub, S., Wilkins, J.A., Rush, D., and Nickerson, P. (2006) Developing a tool for noninvasive monitoring of renal allografts. Expert Rev Proteomics, 3, 497-509.
30. Hortin, G.L. and Sviridov, D. (2007) Diagnostic potential for urinary proteomics. Pharmacogenomics, 8, 237-255.
31. Gonzalez-Buitrago, J.M., Ferreira, L., and Lorenzo, I. (2007) Urinary proteomics. Clin Chim Acta, 375, 49-56.
32. Fliser, D., Novak, J., Thongboonkerd, V., Argiles, A., Jankowski, V., Girolami, M.A., Jankowski, J., and Mischak, H. (2007) Advances in urinary proteome analysis and biomarker discovery. J Am Soc Nephrol, 18, 1057-1071.
33. Schaub, S., Rush, D., Wilkins, J., Gibson, I.W., Weiler, T., Sangster, K., Nicolle, L., Karpinski, M., Jeffery, J., and Nickerson, P. (2004) Proteome-based detection of urine proteins associated with acute renal allograft rejection. J Am Soc Nephrol, 15, 219-227.
34. Koopman, J., Zhang, Z., White, N., Rosenzweig, J., Fedarko, N., Jagannath, S., Canto, M.I., Yeo, C.J., Chan, D.W., and Goggins, M. (2004) Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry. Clin Cancer Res, 10, 860-868.
35. Thulasiraman, V., Lin, S., Gheorghiu, L., Lathrop, J., Lomas, L., Hammond, D., and Boschetti, E. (2005) Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis, 26, 3561-3571.
36. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J., Guerrier, L., Fortis, F., Boschetti, E., Lomas, L., and Righetti, P.G. (2006) Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res, 4, 1917-1930.
37. Fung, E.T., Weinberger, S.R., Gavin, E., and Zhang, F. (2005) Bioinformatics approaches in clinical proteomics. Expert Rev Proteomics, 2, 847-862.
38. Fung, E. and Enderwick, C. (2002) ProteinChip clinical proteomics:computational challenges and solutions. Comput Proteomics, 32, S34-S41.
39. Weinberger, S.R., Boschetti, E., Santambien, P., and Brenac, V. (2002) SELDI - a new method for rapid development of process chromatography conditions. J Chromatogr A, 782, 307-316.
40. Shiloach, J., Santambien, P., Trinh, L., Schapman, A., and Boschetti, E. (2003) Endostatin capture from Pichia pastoris culture in a fluidized bed from on-chip process optimization to application. J Chromatogr A, 790, 327-336.
41. Prahalad, A.K., Hickey, R.J., Huang, J., Hoelz, J., Dobrolecki, L., Murthy, S., Winata, T., and Malkas, L.H. (2006) Serum proteome profiles identifies parathyroid hormone physiologic response. Proteomics, 6, 3482-3493.
42. Thulasiraman, V., McCutchen-Maloney, S.L., Motin, V.L., and Garcia, E. (2001) Detection and identification of virulence factors in Yersinia pestis using SELDI ProteinChip System. BioTechniques, 30, 428-432.
43. Wang, S., Diamond, D.L., Hass, G.M., Sokoloff, R., and Vessella, R.L. (2001) Identification of prostate-specific membrane antigen (PMSA) as the target of monoclonal antibody 107-1A4. Int J Cancer, 92, 871-876.
44. Merchant, M. and Weinberger, S.R. (2000) Recent advancements in surface-enhanced laser desorption-ionization-time of flight-mass spectrometry. Electrophoresis, 21, 1164-1177.
45. Reid, G., Gan, B.S., She, Y.M., Ens, W., Weinberger, S., and Howard, J.C. (2002) Rapid identification of probiotic lactobacillus biosurfactant proteins. Appl Environ Microbiol, 68, 977-980.
46. Clarke, W., Silverman, B.C., Zhang, Z., Chan, D.W., Klein, A.S., and Molmenti, E.P. (2003) Characterization of renal allograft rejection by urinary proteomic analysis. Ann Surg, 237, 660-665.
47. O'Riordan, E., Orlova, T.N., Mei, J., Butt, K., Chander, P.M., Rahman, S., Mya, M., Hu, R., Momin, J., Eng, E.W., Hampel, D.J., Hartman, B., Kretzler, M., Delaney, V., and Goligorsky, M.S. (2004) Bioinformatic analysis of the urinary proteome of acute allograft rejection. J Am Soc Nephrol, 15, 3240-3248.
48. O'Riordan, E., Orlova, T.N., Podust, V.N., Chander, P.N., Yanagi, S., Nakazato, M., Hu, R., Butt, K., Delaney, V., and Goligorsky, M.S. (2007) Characterization of urinary peptide biomarkers of acute rejection I renal allografts. Am J Transplant, 7, 930-940.
49. Jahnukainen, T., Malehorn, D., Sun, M., Lyons-Weiler, J., Bigbee, W., Gupta, G., Shapiro, R., Randhawa, P.S., Pelikan, R., Hauskrecht, M., and Vats, A. (2006) Proteomic analysis of urine in kidney transplant patients with BK virus nephropathy. J Am Soc Nephrol, 17, 3248-3256.
50. Woroniecki, R.P., Orlova, T.N., Mendelev, N., Shatat, I.F., Hailpern, S.M., Kaskel, F.J., Goligorsky, M.S., and O'Riordan, E. (2006) Urinary proteome of steroid-sensitive and steroid-resistant idiopathic nephrotic syndrome syndrome of childhood. Am J Nephrol, 26, 258-267.
51. Khurana, M., Traum, A.Z., Alvado, M., Wells, M.P., Guerrero, M., Grall, F., Libermann, T.A., and Schachter, A.D. (2006) Urine proteomic profiling of pediatric nephrotic syndrome. Pediatr Nephrol, 21, 1257-1265.
52. Mosley, K., Tam, F.W.K., Edwards, R.J., Crozier, J., Pusey, C.D., and Lightstone, L. (2006) Urinary proteomic profiles distinguish between active and inactive lupus nephritis. Rheumatology, 45, 1497-1504.
53. Suzuki, M., Ross, G., Brunner, H., and Devarajan, P. (2006) Identification of signature urinary biomarker patterns in lupus nephritis sub-types. J Am Soc Nephrol, 17, 437A.
54. Rai, A.J., Stemmer, P.M., Zhang, Z., Adam, B.L., Morgan, W.T., Caffrey, R.E., Podust, V.N., Patel, M., Lim, L.Y., Shipulina, N.V., Chan, D.W., Semmes, O.J., and Leung, H.C. (2005) Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry:multi-institution correlation of spectra and identification of biomarkers. Proteomics, 5, 3467-3474.
55. Semmes, O.J., Feng, Z., Adam, B.L., Banez, L.L., Bigbee, W.L., Campos, D., Cazares, L.H., Chan, D.W., Grizzle, W.E., Izbicka, E., Kagan, J., Malik, G., McLerran, D., Moul, J.W., Partin, A., Prasanna, P., Rosenzweig, J., Sokoll, L.J., Srivastava, S., Thompson, I., Welsh, M.J., White, N., Winget, M., Yasui, Y., Zhang, Z., and Zhu, L. (2005) Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin Chem, 51, 102-112.