Application of MALDI/SELDI mass spectrometry to cancer biomarker discovery and validation

Current Proteomics

Volumn 5, Issue 4, 2008, Pages 224-252

  Ahmed, Farid E ^a,b  

^a EAST CAROLINA UNIVERSITY   (United States)

^b GEM Tox Consultants and Labs Inc   (United States)

Author keywords

Bioinformatics; Blood; CSF; Diagnoses; Plasma; Statistics; Urine

Indexed keywords

ANIMALIA;

EID: 57349168191     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016408786733789     Document Type: Review

References (245)

1. Aebersold, R. and Mann, M. (2003). Mass spectrometry-based proteomics. Nature 422: 189-207.
2. Abiko, Y., Nashimura, M. and Kaku, T. (2003). Defensins in saliva and salivary glands. Med. Electron. Microsc. 36: 247-52.
3. Ahmed, F.E. (2006a). Gene-gene, Gene-environment & multiple interactions in colorectal cancer. J. Env. Sci. Health C24: 1-101.
4. Ahmed, F.E. (2006b). Expression microarray proteomics and the search for cancer biomarkers. Curr. Genomics 7: 399-426.
5. *Illustrates the strengths and weakness of microarrays as applied to proteome biomarker discovery.
6. Ahmed, F.E. (2006c). Laser microdissection: application to carcinogenesis. Cancer Genom. Proteom. 3: 217-26.
7. *Illustrates the application of microdisscection techniques for cell selection. Ahmed, F.E. (2008a). Mining the oncoproteome and studying molecular interactions for biomarker development by 2DE, ChIP and SPR technologies. Exp. Rev. Proteomics 5: 469-96.
8. *Detailed treatment of some proteomic procedures for biomarker discovery.
9. Ahmed, F.E. (2008b). Utility of mass spectrometry for proteome analysis: Part I. Conceptual and experimental approaches. Exp. Rev. Proteomics 5 "in press".
10. *Comprehensive evaluation of various mass spectrometers and ionization methods.
11. Ahmed, F.E. (2009a). The role of capillary electrophoresis-mass spectrometry in protein analysis and biomarker discovery. J. Chromatogr. B "in press".
12. *Details use of CE-MS for biomarker discovery.
13. Ahmed, F.E. (2009b). Sample preparation and fractionation for proteome analysis by mass spectrometry. J. Sep. Sci. 32 "in press".
14. *Details methods of sample preparation and fractionation.
15. Ahmed, F.E. (2009c). Utility of mass spectrometry for proteome analysis: II. Statistics, bioinformatics and annotation. Exp. Rev. Proteomics 6 "in press".
16. *Concise treatment of data analysis and ontology in proteomics.
17. Akewanlop, C., Watanabe, M., Singh, B., Walker, M., Kufe, D.W. and Hayes, D.F. (2001). Phagocytosis of breast cancer cells mediated by anti-MUC-1 monoclonal antibody, DF3, and its bispecific antibody. Cancer Res. 61: 4061-5.
18. Albrethesen, J. (2007). Reproducibility in protein profiling by MALDI-TOF mass spectrometry. Clin. Chem. 53: 852-8.
19. Anderson, N.L. (2005). The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol. Cell. Proteomics 4: 1441-4.
20. Anderson, N.L. and Anderson, N.G. (2002). The human plasma proteome: history, character, and dagnostic prospects. Mol. Cell. Proteomics 1: 845-67.
21. Anderson, N.L., Anderson, N.G., Haines, L.R., Hardie, D.B., Olafson, R.W. and Pearson, T.W. (2004). Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J. Proteome Res. 3: 235-44.
22. Anderson, L. and Hunter, C.L. (2006). Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5: 573-88.
23. Anderson, N.L., Polanski, M., Pieper, R., Gatlin, T., Tirumali, R.S., Conrads, T.P., Veenstra, T.D., Adkins, J.N., et al. (2004). The human plasma proteome: a nonredundant list developed by combination of four separate souces. Mol. Cell. Proteomics 3: 311-26.
24. Andriani, F., Conte, D., Mastrangelo, T., Leon, M., Ratcliffe, C., Roz, L., Pelosi, G., Goldstraw, P., et al. (2004). Detecting lung cancer in plasma with the use of multiple genetic markers. Int J. Cancer 108: 91-6.
25. Barker, P.E., Wagner, P.D., Stein, S., Bank, D.M, Srivastava, S. and Omenn, G.S. (2006). Standards for plasma and serum proteomics in early cancer detection: a needs assessment report from the National Institute of Standards and Technology-National Cancer Institute Standards, methods, assays, reagents and technologies workshop, August 18-19, 2005. Clin. Chem. 52: 1669-74.
26. Blow, N. (2008). Mass spectrometry and proteomics: hitting the mark. Nat. Methods 5: 741-7.
27. Booner, K., Landuyt, B., Baggerman, G., Husson, S.J., Huybrechts, J., Schoofs, L. (2008). Peptidomics: The integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis. J. Sep. Sci. 31: 427-45.
28. Brown, M.P., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Funey, T.S., Ames, M. and Haussler, D. (2000). Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. USA 97: 262-7.
29. Cadieux, P.A., Beiko, D.T., Watterson, J.D., Burton, J.P., Howard, J.C., Knudsen, B.E., Gan, B.S., McCormick, J.K., et al. (2004). 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. 18: 170-5.
30. Caňas, B., Pineiro, C., Calvo, E., López-Ferner, D. and Gallardo, J.M. (2007). Trends in sample preparation for classical and second generation proteomics. J. Chromatogr. A. 1153: 235-58.
31. Carlsson, S. (1973). Fibrinogen degradation products in serum from patients with cancer. Acta. Chir. Scand. 139: 499-502.
32. Carrette, O., Demalte, I., Scherl, A., Yalkinoglu, O., Corthals, G., Burkhard, P., Hochstrasser, D.F. and Sanchez, J. (2003). A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease. Proteomics 3: 1486-94.
33. Castagna, A., Cecconi, D., Sennels, L., Rappsilber, J., Lomas, L. and Righetti, P.G. (2005). Exploring the hidden human urinary proteome via ligand library beads. J. Proteome. Res. 4: 1917-30.
34. Celis, A., Rasmussen, H.H., Celis, P., Basse, B., Lauridsen, J.B., Ratz, G., Hein, B., Ostergaard, M., et al. (1999). Short-term culturing of low-grade superficial bladder transitional carcinoma leads to changes in the expression levels of several proteins involved in key cellular activities. Electrophoresis 20: 355-61.
35. Chalmers, M.J., Mackay, C.L., Hendrickson, C.L., Wittke, S., Walden, M., Mischak, H. and Marshall, A.G. (2005). Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease. Anal. Chem. 77: 7163-71.
36. Chait, B.T. (2006). Mass spectrometry: bottom-up or top-down? Science 314: 65-6.
37. Chen, G. and Pramanik, B.N. (2008). LC-MS for protein characterization: current capabilities and future trends. Exp. Rev. Proteomics 5: 435-44.
38. Chevallet, M., Diemer, H., van Dorsselaer, A., Villers, C. and Rabilloud, T. (2007). Towards a better analysis of secreted proteins: the example of the myeloid cell secretome. Proteomics 7: 1757-70.
39. 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: 660-4.
40. Codero, M.M., Cornish, T.J., Cotter, R.J. and Lys, I.A. (1995). Sequencing peptides without scanning the reflectrons: post-source decay with a curved-field reflectron time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 91: 1356-61.
41. Conrads, T.P., Fusaro, V.A., Ross, S., Johann, D., Rajapakse, V., Hitt, B.A., Steiberg, S.M., Kohn, E.C., et al. (2004). High resolution serum proteomic features for ovarian cancer detection. Endocr. Relat. Cancer 11: 163-78.
42. Conrads, T.P., Hood, B.L. and Veenstra, T.D. (2006). Sampling and analytical strategies for biomarker discovery using mass spectrometry. Bio Techniques 40: 799-805.
43. Cotter, R.J. (1992). Time-of-flight mass spectrometry for the structural analysis of biological molecules. Anal. Chem. 64: 1027A-39.
44. Cserr, H.F., Cooper, D.N., Suri, P.K. and Patlak, C.S. (1981). Efflux of radiolabeled polyethylene glycols and albumin from rat brain. Am. J. Physiol. 240: F319-28.
45. Dalton, W.S. and Friend, S.H. (2006). Cancer biomarkers-an invitation to the table. Science 312: 1165-58.
46. D'Amico, G. and Bazzi, C. (2007). Pathophysiology of proteinuria. Kidney Int. 63: 809-25.
47. Davidson, P., Espina, V., Steinberg, S.M., Flørenes, V.A., Liotta, L.A., Kristensen, G.B., Trope, C.G., Berner, A., et al. (2006). Proteomic analysis of malignant ovarian cancer effusions as a tool for biologic and prognostic profiling. Clin. Cancer Res. 12: 791-9.
48. Dare, T.O., Davies, H.A., Turton, J.A., Lomas, L., Williams, T.C. and York, M.J. (2002). Application of surface-enhanced laser desorption/ ionization technology to the detection and identification of urinary parvalbumin-alpha: a biomarker of compound-induced skeletal muscle toxicity in the rat. Electrophoresis 23: 3241-51.
49. Dawson, N.N. (1999). Response criteria in prostatic carcinoma. Semin. Oncol. 26: 174-84.
50. De Masi, F., Chiarella, P., Wilhelm, H., Massimi, M., Bullard, B., Ansorge, W. and Sawyer, A. (2005). High throughput production of mouse monoclonal antibodies using antigen microarrays. Proteomics 5: 4070-81.
51. de Noo, M.E., Deelder, A., van der Werff, M., Özlap, A., Mertens, B. and Tollenaar, R. (2006). MALDI-TOF serum protein profiling for the detection of breast cancer. Onkologie 29: 501-6.
52. Diamandis, E.P. (2004). Mass spectrometry as a diagnostic and a cancer biomarker discovery tool. Mol. Cell. Proteomics 3: 367-78.
53. Diamandis, E.P. (2006a). Peptidomics for cancer diagnosis: present and future. J. Proteome Res. 5: 2079-82.
54. Diamandis, E.P. (2006b). Serum proteomic profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for cancer diagnosis: next steps. Cancer Res. 66: 5540-1.
55. Diamandis, E.P. (2007). Oncopeptidomics: a useful approach for cancer diagnosis? Clin. Chem. 53: 1004-6.
56. Diamandis, E.P. and Yousef, G.M. (2002). Human tissue kallikreins: a family of new cancer biomarkers. Clin. Chem. 48: 1198-205.
57. Dihazi, H., Muller, G.A., Lindner, S., Meyer, M., Asif, A.R., Oellerich, M. and Stratz, F. (2007). Characterization of diabetic nephropathy by urinary proteomic analysis: identification of a processed ubiquitin form as a differentially excreted protein in diabetic nephropathy patients. Clin. Chem. 53: 1636-45.
58. Engwegen, J.Y.M.N., Gast, M-C.W., Schellens, J.H.M. and Beijnen, J.H. (2006). Clinical proteomics: searching for better tumor markers with SELDI-TOF mass spectrometry. Trends Pharm. Sci. 27: 251-9.
59. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F. and Whitelhouse, C.M. (1989). Electrospray ionization for the mass spectrometry of large biomolecules. Science 246: 64-71.
60. Feuerstein, I., Najam-ul-Haq, M., Rainer, M., Trojer, L., Bakry, R., Aprilita, N.H., Stecher, G., Huck, C.W., et al. (2006). Material enhanced laser desorption/ionization (MELDI) -a new protein profiling tool utilizing specific carrier materials for time of fliht mass spectrometric analysis. J. Am. Soc. Mass Spectrom. 17: 1203-8.
61. Fortier, A.H., Holaday, J.W., Liang, H., Dey, C., Grella, D.K., Holland-Linn, J., Vu, H., Plum, S.M., et al. (2003). Recombinant prostate specific antigen inhibits angiogenesis in vitro and in vivo. Prostate 56: 212-9.
62. Fung, E.T., Weinberger, S.R., Gavin, E. and Zhang, F. (2005). Bioinformatics approaches in clinical proteomics. Expert Rev. Proteomics 2: 847-62.
63. *Illustration of the application of statistics and bioinformatics methods in clinical proteomic studies.
64. Garguso, I. and Borlak, J. (2008). Matrix layer sample preparation: an improved MALSI-MS peptide analysis method for proteomic studies. Proteomics 8: 2583-95.
65. Gasparini, G. and Gion, M. (2000). Molecular-targeted anticancer therapy: challenges related to study design and choice of proper endpoints. Cancer J. Sci. Am. 6: 117-31.
66. Gatlin, C.L., Kleemann, G.R., Hays, L.G., Link, A.J. and Yates, J.R.III. (1998). Identification at the low femtomole level from silver-stained gels using anew fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Chem. 263: 93-101.
67. Gion, M. and Daidone, M.G. (2004). Circulating biomarkers from tumor bulk to tumor machinery: promises and pitfalls. Eur. J. Cancer 40: 2613-22.
68. Giovannucci, E. (1999). Insulin-like growth factor-I and binding protein-3 and risk of cancer. Horm. Res. 51: 34-41.
69. Goldstein, L.E., Muffat, J.A., Cherny, R.A., Moir, R.D., Ericsson, M.H., Huang, X., Mavros, C., Coccia, J.A., et al. (2003). Cytosolic beta-amyloid deposition and supranuclear cataracts in lenses from people with Alzheimer's disease. Lancet 361: 1258-65.
70. Good, D.M., Thongboonkerd, V., Novak, J., Bascands, J.L., Schanstra, J.P., Coon, J.J., Dominiczak, A. and Mischak, H. (2007). Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J. Proteome Res. 6: 4549-55.
71. Graham, D.R.M., Elliott, S.T. and Van Eyk, J.E. (2004). Broad-based proteomic strategies: a practical guide to proteomics and functional screening. J. Physiol. 563: 1-9.
72. Gundry, R.L., Fu, Q., Jelinek, C.A., Van Eyk, J.E. and Cother, R.J. (2007). Investigation of an albumin-enriched fraction of human serum and its albuminome. Proteomics Clin. Apll. 1: 73-88.
73. Hampel, D.J., Sansome, C., Sha, M., Brodsky, S., Lawson, W.E. and Goligorsky, M.S. (2001). Towards proteomics in uroscopy: using protein profiles after radiocontrast media administration. J. Am. Soc. Nephrol. 12: 1026-35.
74. Han, D.K. (2007). Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 26: 65-76.
75. Haoudi, A. and Bensmail, H. (2006). Bioinformatics and data mining in proteomics. Exp. Rev. Proteomics 3: 333-43.
76. Henzel, W.J., Watanabe, C. and Stults, J.T. (2003). Protein identification: the origins of peptide mass fingerprinting. J. Am. Soc. Mass Spectrom. 14: 931-42.
77. Hernádez-Borges, J., Neussüs, C., Cifuentes, A. and Pelzing, M. (2004). On-line capillary electrophoresis-mass spectrometer gor the analysis of biomolecules. Electrophoresis 25: 2257-81.
78. Hoffmann, S.A., Joo, W.A., Echan, L.A. and Speicher, D.W. (2007). Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J. Chromatogr. B. 849: 43-52.
79. Hortin, G.L. (2006). The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin. Chem. 52: 1223-37.
80. Hsu, W.Y., Lo, W.Y., Lai, C.C., Tsai, F.J., Tsai, C.H., Tsai, Y., Lin, W.D. and Chao, M.C. (2007). Rapid screening assay of trimethylaminuria in urine with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 21: 1915-9.
81. Hu, S., Loo, J.A. and Wong, D.T. (2006). Human body fluid proteome analysis. Proteomics 6: 6326-53.
82. Hutchens, T.W. and Yip, T.T. (1992). Synthetic metal-binding protein surface domains for metal ion-dependent interaction chromatography. J. Chromatogr. 604: 133-41.
83. Hwang, S-I., Thumar, J., Lundgren, D.H., Rezaul, K., Mayya, V., Wu, L., Eng, J., Wright, M.E., et al. (2001). Germ line mutations associated with breast cancer susceptibility. Eur. J. Cancer 37: 300-21.
84. Issaq, H.J. and Veenstra, T.D. (2007). The role of electrophoresis in disease biomarker discovery. Electrophoresis 28: 1980-8.
85. Issaq, H.J., Xiao, Z. and Veenstra, T.D. (2007). Serum and plasma proteomics. Chem. Rev. 107: 3601-20.
86. Iwaki, H., Kageyama, S., Isono, T., Wakabagashi, Y., Okada, Y., Yoshimura, K., Terai, A., Arai, Y., et al. (2004). Diagnostic potential in bladder cancer of a panel of tumor markers (calreticulin, gamma-synuclein and catechol-o methylttransferase) identification by proteomic analysis. Cancer Sci. 95: 955-61.
87. Jackson, E.L., Olive, K.P., Tuveson, D.A., Bronson, R., Crowley, D., Brown, M. and Jacks, T. (2005). The differential effects of mutant p53 alleles on advanced murine lung cancer. Cancer Res. 65: 10280-8.
88. Jahnukainen, T., Malehorn, D., Sun, M., Lyons-Weiler, J., Bighbee, W., Gupta, G., Shapiro, R., Randhawa, P.S., et al. (2006). Proteomic analysis of urine in kidney transplant patients with BK virus nephropathy. J. Am. Soc. Nephrol. 17: 3248-56.
89. Johann, D.J.Jr. and Veenstra, T.D. (2007). Multiple biomarkers in molecular biology. Exp. Rev. Mol. Diag. 7: 223-5.
90. Jorgenson, J.W. and Luckacs, K.D. (1983). Capillary zone electrophoresis. Science 222: 266-72.
91. Jurgens, M., Appel, A., Heine, G., Neitz, S., Menzel, C., Tammen, H. and Zucht, H.T. (2005). Towards characterization of the human urinary peptidome. Comb. Chem. High Throughput Screen. 8: 757-65.
92. Kageyama, S., Isono, T., Iwaki, H., Wakabayashi, Y., Okada, Y., Kontani, K., Yoshimura, K., Terai, A., et al. (2004). Idenfification by proteomic analysis of caltreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine. Clin. Chem. 50: 857-66.
93. Kaiser, T., Hermann, A., Kielstein, J.T., Wittke, S., Bartel, S., Krebs, R., Hausadel, F., Hillmann, M., et al. (2003). Capillary electrophoresis coupled to mass spectrometry to establish polypeptide patterns in dialysis fluids. J. Chromatogr. A. 1013: 157-71.
94. Kaiser, T., Wittke, S., Just, I., Krebs, R., Bartel, S., Fliser, D., Mischak, H. and Weissinger, E.M. (2004). Capillary electrophoresis coupled to mass spectrometer for automated and robust polypeptide determination in body fluid for clinical use. Electrophoresis 25: 2044-55.
95. Karas, M., Gluckmann, M. and Schafer, J. (2000). Ionization in matrix-assisted laser desorption/ ionization: singly charged molecular ions are the lucky survivors. J. Mass Spectrom. 35: 1-12.
96. Karas, M. and Hillenkamp, F. (1988). Laser desorption ionization of proteins with molecular mass exceeding 10000 daltons. Anal. Chem. 60: 2299-301.
97. Karasan, A., Eigl, B.J., Flibotte, S., Gelmon, K., Switzer, P., Hassell, P., Harrison, D., Law, J., et al. (2005). Analytical and preanalytical biases in serum proteomic pattern analysis for breast cancer diagnosis. Clin. Chem. 51: 1525-8.
98. Karlsson, R. (2004). SPR for molecular interaction analysis: a review of emerging application areas. J. Mol. Recognit. 17: 151-61.
99. Kemna, E.H., Tjalsma, H., Podust, V.N. and Swinkets, D.W. (2007). Mass spectrometry-based hepcidin measurements in serum and urine: analytical aspects and clinical applications. Clin. Chem. 53: 620-8.
100. Khurana, M., Traum, A.Z., Aivado, M., Wells, M.P., Guerreno, M., Grall, F., Libermann, T.A. and Schachler, A.D. (2006). Urine proreomic profiling of pediatric nephritic syndrome. Pediatr. Nephrol. 21: 1257-65.
101. Kiernan, U.A. (2007). Quantitation of target proteins and post-translation modifications in affinity-based proteomic approaches. Exp. Rev. Proteomics 4: 421-8.
102. Kiernan, U.A., Nedelkov, D., Tubbs, K.A., Niederkofler, E.E. and Nelson, R.W. (2004). Proteomic characterization of normal serum amyloid P component variant from human plasma and urine. Proteomics 4: 1825-9.
103. Kiernan, U.A., Tubbs, K.A., Gruber, K., Nedelkov, D., Niederkotler, E.E. and Nelson, R.W. (2002). Comparative analysis of human plasma and urinary retinol binding protein using mass spectrometric immunoassay. Biochim. Biophys. Res. Commun. 297: 401-5.
104. Kiernan, U.A., Tubbs, K.A., Nedelkov, D., Niederkofler, E.E., McConnell, E. and Nelson, R.W. (2003). Comparative urine protein phenotyping using mass spectrometric immunoassay. J. Proteome Res. 2: 191-7.
105. Kolch, W., Neusüss, C., Pelzing, M. and Mischak, M. (2005). Capillary electrophoresis-mass spectrometry as a powerful tool in clinical urinalysis and biomarker discovery. Mass Spectrom. Rev. 24: 959-77.
106. *Illustrates the role of CE-MS in urinary biomarker research. Koomen, J.M., Li., D., Xiao, L-C., Liu, T.C., Coombes, K.R., Abbruzzese, J. and Kobayashi, R. (2005). Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J. Proteome Res. 4: 972-81.
107. Kosanam, H., Prakash, P.K., Yates, C.R., Miller, D.D. and Ramagiri, S. (2007). Rapid screening of doping agents in human urine by vaccum MALDI-linear ion trap mass spectrometry. Anal. Chem. 79: 6020-6.
108. Krone, J.R., Nelson, R., Williams, P., Nelson, R.W., Dogruel, D., Krone, J.R. and Williams, P. (1995). Peptide characterization using bioactive mass spectrometer probe tips. Rapid Commun. Mass Spectrom. 9: 1380-1885.
109. Krueger, K.E. (2006). The potential of serum peptidomics for detection of cancer: promise or only hope? Onkologie 29: 498-9.
110. Kussmänn, M., Raymond, F. and Affolter, M. (2006). OMICS-driven biomarker discovery in nutrition and health. J. Biotechnol. 124: 758-87.
111. Kuster, B., Schirle, M., Mallick, P. and Aebersold, R. (2005). Scoring proteomes with proteolytic peptide proteome. Nat. Rev. Mol. Cell. Biol. 6: 577-83.
112. Laugesen, S. and Roepstorff, P. (2003). Combination of two matrices results in improved performance of MALDI MS for peptide mass mapping and protein analysis. J. Am. Soc. Mass Spectrom. 14: 992-1002.
113. Lawrie, L.C., Fothergill, J.E. and Murray, G.I. (2001). Spot the differences: proteomics in cancer research. Lancet Oncol. 2: 270-7.
114. Lewczuk, P., Esselman, H., Groemer, T.W., Bibl, M., Maler, J.M., Steinacker, P., Otto, M., Kornbuber, J., et al. (2004). Amyloid beta peptides in cerebrospinal fluid as profiled with surface enhanced laser desorption/ionization time-of-flight mass spectrometry: evidence of normal biomarkers in Alzheimer's disease. Biol. Psychiatry 55: 524-30.
115. Lescuyer, P., Hochstrasser, D. and Rabilloud, T. (2007). How should we use the proteomic toolbar for biomarker discovey. J. Proteome Res. 6: 3371-6.
116. Lewczuk, P., Esselman, H., Meyer, M., Wollscheid, V., Neumann, M., Otto, M., Maler, J.M., Ruther, E., et al. (2003). The amyloid-beta (Abeta) peptide pattern in cerebrospinal fluid in Alzheimer's disease: evidence of a novel carboxyterminally elongated Abeta peptide. Rapid Commun. Mass Spectrom. 17: 1291-6.
117. Li, J., Orlandi, R., White, C.N., Rosenzweig, J., Zhao, J., Seregni, E., Morelli, D., Yu, Y., et al. (2005). Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin. Chem. 51: 2229-35.
118. Lida, R., Yasuda, T. and Kishi, K. (2007). Identification of novel fibronectin fragments detected specifically in juvenile urine. FEBS J. 274: 3939-47.
119. Lilja, H., Oldbring, J., Rannevik, G. and Laurell, C.B. (1987). Seminal vesicle-secreted proteins and their reactions during gelation and lique-faction of human semen. J. Clin. Invest. 80: 281-5.
120. Lim, M.S. and Elenitoba-Johnson, K.S.J. (2004). Proteomics in pathology research. Lab. Invest. 84: 1227-44.
121. Linke, T., Doraiswamy, S. and Harison, E.H. (2007). Rat plasma proteomics: effects of abundant protein depletion on proteomic analysis. J. Chromatography B. 849: 273-81.
122. Liotta, L.A., Ferrari, M. and Petricoin, E. (2003). Clinical proteomics: written in blood. Nature 425: 905.
123. Liotta, L.A. and Petricoin, E.F. (2006). Serum peptidome for cancer detection: spinning biological trash into diagnostic gold. J. Clin. Invest. 116: 26-30.
124. Liotta, L.A. and Petricoin, E.F. (2008). Putting the "bio" back into biomarkers: orienting proteomic discovery toward biology and away from the measurement platform. Clin. Chem. 54: 3-5.
125. Lopez, M.F., Mikulskis, A., Kuzdzal, S., Golenko, E., Petricoin, E.F. 3rd, Liotta, L.A., Patton, W.F., Whitele, G.R., et al. (2007). A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cance samples. Clin. Chem. 53: 1067-74.
126. Lum, G. and Gambino, S.R. (1974). Comparison of serum versus heparinized plasma for routine chemistry tests. Am. J. Clin. Pathol. 61: 108-13.
127. Magi, B., Bargagli, E., Bini, L. and Rottoli, P. (2006). Proteome analysis of brochoalveolar lavage in lung diseases. Proteomics 6: 6354-69.
128. Marcus, K., Schäfer, H., Klaus, S., Bunse, C., Swart, R. and Meyer, H.E. (2007). A new fast method for nanoLC-MALDI-TOF/TOF-MS analysis using monolithic columns for peptide preconcentration and separation in proteomic studies. J. Proteome Res. 6: 635-43.
129. Martinovic, S., Veenstra, T.D., Anderson, G.A., Pasa-Tolic, L. and Smith, R.D. (2002). Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome-wide level. J. Mass Spectrom. 37: 99-107.
130. Maxwell, P. (1999). Carcinoembryonic antigen: cell adhesion molecule an useful diagnostic marker. Br. J. Biomed. Sci. 56: 209-14.
131. Mclerran, D., Grizzle, W.E., Feng, Z., Bigbee, W.L., Banez, L.L., Cazares, L.H., Chan, D.W., Diaz, J., et al. (2008a). Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias. Clin. Chem. 54: 44-52.
132. Mclerran, D., Grizzle, W.E., Feng, Z., Thompson, I.M., Bigbee, W.L., Cazares, L.H., Chan, D.W., Dahlgren, J., et al. (2008b). SELDI-TOF MS whole serum proteomic profiling with IMAc surface does not reliably detect prostate cancer. Clin. Chem. 54: 53-60.
133. Mischak, H., Apweiler, R., Banks, R.E., Conaway, M., Coon, J., Dominiczak, A., Ehrich, J.H.H., Fliser, D., et al. (2007). Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin. Appl. 1: 148-56.
134. M'koma, A.E., Blum, D.L., Norris, J.L., Koyama, T., Billheimer, D., Motley, S., Ghiassi, M., Ferdowsi, N., et al. (2003). Detection of preneoplastic and neoplastic prostate disease by MALDI profiling of urine. Biochem. Biophys. Res. Commun. 353: 829-934.
135. Moe, O.W., Wright, S.H. and Palacin, M. Renal handling of organic colvents. (2008). Brenner & Rector's The Kidney. 8th ed. (Brenner, B.M. Ed.). Saunders Elsevier, Philadelphia, PA, pp. 214-47.
136. Mosley, K., Tam, F.W., Edwards, R.J., Crozier, J., Pausey, C.D. and Lightstone, L. (2006). Urinary proteomic profiles distinguish between active and inactive lupus nephritis. Rheumatology 45: 1497-504.
137. Moss, E.L., Hollingworth, J. and Reynolds, T.M. (2006). The role of CA125 in clinical practice. J. Clin. Pathol. 58: 308-12.
138. Moulay, A.-J. and Xing-Jie, X. (2006). Proteomic technology for biomarker profiling in cancer: an update. J. Zhejiang Univ. Sci. B 7: 411-20.
139. Mueller, J., von Eggeling, F., Driesch, D., Schubert, J., Melle, C. and Junker, K. (2005). ProteinChip technology reveals distinctive protein expression profiles in the urine of bladder cancer patients. Eur. Urol. 47: 885-93.
140. Munro, N.P., Cairns, D.A., Clarke, P., Rogers, M., Stanley, A.J., Barrett, J.H., Harnden, P., Thompson, D., et al. (2006). Urinary biomarker profiling in transitional carcinoma. Int. J. Cancer 119: 2642-50.
141. Mushtaq, S., Siddiqui, A.A., Naqvi, Z.A., Rattani, A., Talati, J., Palmberg, C. and Shafqat, J. (2007). Identification of myeloperoxidase, alfadefensin and calgranulin in calcium oxalate renal stone. Clin. Chim. Acta 384: 41-7.
142. Najam-ul-Haq, M., Rainer, M., Heigl, N., Szabo, Z., Vallant, R., Huck, C.W., Engelhardt, H., Bischoff, K.D., et al. (2008). Nano-structured support material, their characterization and serum protein profiling through MELDI/TOF-MS. Amino Acids 34: 279-86.
143. Najam-ul-Haq, M., Rainer, M., Trojer, L., Feuerstein, I., Vallant, R.M., Huck, C.W., Bakry, R. and Bonn, G.K. (2007). Alternative profiling platform based on MELDI and its applicability in clinical proteomics. Exp. Rev. Proteomics 4: 447-52.
144. *Illustration of the use of MELDI platform for improved proteome analysis in clinical samples.
145. Nedelkov, D., Kiernan, U.A., Niederkofler, E.E., Tubbs, A. and Nelson, R.W. (2006). Population proteomics: The concepts, attributes, and potential for cancer biomarker research. Mol. Cell. Proteomics 5: 1811-8.
146. Nedelkov, D., Tubbs, K.A., Niederkofler, E.E. and Nelson, R.W. (2004). High-throughput comprehensive analysis of human plasma: a step towards population proteomics. Anal. Chem. 76: 1733-7.
147. Nice, E.C., Rothacker, J., Weinstock, J., Lim, L. and Catmiel, B. (2007). Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomic analysis. J. Chromatogr. A. 168: 190-210.
148. Nguyen, M.T., Ross, G.F, Dent, C.L. and Devarajan, P. (2005). Early prediction of active renal injury using urinary proteomics. Am. J. Nephrol. 25: 318-26.
149. Omenn, G.S., States, D.J., Adamski, M., Blackwell, T.W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B.B., et al. (2005). Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5: 3226-45.
150. O'Riordan, E., Orlova, T.N., Podust, V.N., Chander, P.N., Yanagi, S., Nakazato, M., Hu, R., Butt, K., et al. (2007). Characterization of urinary peptide biomarkers of acute rejection in renal allografts. Am. J. Transplant. 7: 930-40.
151. Ornstein, D.K., Englert, C., Gillespie, J.W., Paweletz, C.P. and Linehan, W.M. (2000). Characterization of intracellular prostate specific antigen from laser capture microdissected benign and malignant prostatic epithelium. Clin. Cancer Res. 6: 353-6.
152. Otu, H.H., Can, H., Spentzos, D., Nelson, R.G., Hanson, R.L., Looker, H.C., Knowles, W.C., Monroy, M., et al. (2007). Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy. Diabetes Care 30: 638-43.
153. Palagi, P.M., Walther, D., Quadroni, M., Sébastien, C., Burgess, J. and Appel, R.D. (2005). MSight: an image analysis software for liquid chromatography-mass spectrometry. Proteomics 5: 2381-4.
154. Papale, M., Pedicillo, M.C., Thatcher, B.J., Di Paolo, S., Lo, Muzio, L., Bufo, P., Rocchetti, M.T., et al. (2007). Urinary profiling by SELDITOF/ MS: monitoring of the critical steps in sample collection, handling and analysis. J. Chromatogr. B. 856: 205-13.
155. Pappin, D.J.C., Hojrup, P. and Bleasby, A.J. (1993). Rapid identification of proteins by peptide mass fingerprinting. Curr. Biol. 3: 327-32.
156. Pepe, M.S., Etzioni, R., Feng, Z., Potter, J.D., Thompson, M.L., Thornquist, M., Winget, M. and Yasui, Y. (2001). Phases of biomarker development for early detection of cancer. J. Natl. Cancer Inst. 93: 1054-61.
157. Petersen, G.M., Brensinger, J.D., Johnson, K.A. and Giardiello, F.M. (1999). Genetic testing and counseling for hereditary forms of colorectal cancer. Cancer 86 (11 Suppl.): 2540-50.
158. Petricoin, E.F. and Liotta, L.A. (2004). Clinical proteomics: application at bed side. Contrib. Nephrol. 141: 93-103.
159. Petricoin, E.F.III, Zoon, K.C., Kohn, E.C., Barrett, J.C. and Liotta, L.A. (2002). Clinical proteomics: translating benchside promise into bedsite reality. Nature Rev. Drug Discov. 1: 683-95.
160. Piper, R., Gatlin, C.L., McGrath, A.M., Makusky, J.A., Mondal, M., Seonarain, M., Field, E., Schatz, C.R., et al. (2004). Characterization of the human urinary proteome: a method for high resolvation display of urinary proteins on two-dimensional gel electrophoresis with a yield of nearly 1400 distinct protein spots. Proteomics 4: 1159-74.
161. Pisitkun, T., Johnstone, R. and Knepper, M.A. (2006). Discovery of urinary biomarkers. Mol. Cell. Proteomics 5: 1760-71.
162. Prakash, A., Piening, B., Whiteakers, J., Zhang, H., Shaffer, S.A., Martin, D., Hohmann, L., Cookes, K., et al. (2007). Assessing bias in experimental design for large scale mass spectrometry-based qualitative proteomics. Mol. Cell. Proteomics 6: 1741-8.
163. Pugia, M.J., Jortani, S.A., Basu, M., Sommer, R., Kuo, H.H., Murphy, S., Williamson, D., Vranish, J., et al. (2007). Immunologic evaluation of urinary trypsin inhibitors in blood and urine: role of N-εt-o-linked glycoproteins. Glycoconjugate J. 24: 5-15.
164. Qu, Y., Adam, B.L., Thornquist, M., Potter, J.D., Thompson, M.L., Yasui, Y., Davis, J., Schellhamer, P.F., et al. (2003). Data reduction using a discrete wavelet transform in discriminant analysis of very high dimensionality data. Biometrics 59: 143-51.
165. Rai, A.J., Gelfand, C.A., Haywood, B.C., Warunek, D.J., Yi, J., Schuchard, M.D., Mehigh, R.J., Cockrill, S.L., et al. (2005). HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5: 3226-377.
166. Ranshoff, D.F. (2003). Developing molecular biomarkers for cancer. Science 299: 1679-81.
167. Ranshoff, D.F. (2005). Bias as a threat to the validity of cancer molecular marker research. Nature Rev. Cancer 5: 142-9.
168. *Explains what is meant by bias and how it can be introduced in cancer biomarker research.
169. Resor, L., Bowen, T.J. and Wynshaw-Boris, A. (2001). Unraveling human cancer in the mouse: recent refinements to modeling and analysis. Hum. Mol. Genet. 10: 669-75.
170. Reyzer, M.L. and Caprioli, R.M. (2007). MALDI-MS-based imaging of small molecules and proteins in tissues. Curr. Opin. Chem. Biol. 11: 29-35.
171. Rifai, N., Gillette, M.A. and Carr, S.A. (2006). Protein biomarker
172. *Comprehensive treatment of the topic of biomarker from the discovery to the validation phase.
173. Robijn, M.L., Koeleman, C.A., Hokke, C.H. and Deelder, A.M. (2007a). Schistosoma mansoni eggs excrete specific free oligosaccharides that are detectable in the urine of the human host. Mol. Biochem. Parasitol. 151: 162-72.
174. Robijn, M.L., Koeleman, C.A., Wuhrer, M., Royle, L., Geyer, R., Dwek, R.A., Rudd, P.M., Deelder, A.M., et al. (2007b). Targeted identification of a unique glycan epitope of Schistosoma mansoni egg antigens using a diagnostic antibody. Mol. Biochem. Parasitol. 151: 148-61.
175. Robijn, M.L., Planken, J., Kornelis, D., Hokke, C.H. and Deelder, A.M. (2008). Mass spectrometric detection of urinary oligosaccharides as markers of Schistosoma mansoni infection. Trans. Roy. Soc. Trop. Med. Hyg. 102: 79-83.
176. Rogers, M.A., Clarke, P., Noble, J., Munro, N.P., Paul, A., Selby, P.J. and Banks, R.E. (2003). Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res. 63: 6971-83.
177. Sackett, D.L. and Haynes, R.B. (2002). The architecture of diagnostic research. Br. Med. J. 324: 539-41.
178. Satten, G.A., Datta, S., Moura, H., Wolfitt, A.R., Carvalho, M., Garlone, G.M., De, B.K., Pavlopoulos, A. and Barr, J.R. (2004). Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens. Bioinformatics 20: 3128-36.
179. Schaub, S., Wilkins, J.A., Antonovici, M., Krokhlin, O., Weiler, T., Rush, D. and Nickerson, P. (2005). Proteomic-based identification of cleaved urinary beta z-macroglobulin as a potential marker for acute tubular injury in renal allografts. Am. J. Transplant. 5: 729-38.
180. Schaub, S., Wilkins, J., Weiler, T., Sangster, K., Rush, D. and Nickerson, P. (2004). Urinary protein profiling with surface-enhanced-laser desorption/ ionization time-of-flighy mass spectrometry. Kidney Int. 65: 323-32.
181. Schiffer, E., Mischak, H. and Novak, J. (2006). High resolution proteome/ peptide analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics 6: 5615-27.
182. Schmidt, A. and Aebersold, R. (2006). High-accuracy proteome map of human body fluids. Genome Biol. 7: 241.
183. Service, R.F. (2008). Proteomics ponders prime time. Science 321: 17581-61.
184. Semmes, O.J., Feng, Z., Adam, B.L., Banez, L.L., Bigbee, W.L., Campos, D., Cazares, L.H., Chan, D.W., et al. (2005). Assessment of platform reproducibility. Clin. Chem. 51: 102-12.
185. Shou, Z., Wu, J. and Zheng, S. (2008). Diagnosis of renal allograft subclinical rejection by urine protein fingerprint analysis. Transplant. Immunol. 18: 255-9.
186. Shui, H.A., Huang, T.H., Ka, S.M., Chen, P.H., Lin, Y.F. and Chen, A. (2008). Urinary proteome and potential biomarkers associated with serial pathogenesis steps of focal segmentation glomerulosclerosis. Nephrol. Dialysis Transplant. 23: 176-85.
187. Silva, J.C., Gornestein, M.V., Li, G-Z., Vissers, J.P.C. and Geromanos, S.J. (2006). Absolute quantification of proteins by LCMS. A virtue of parallel MS acquisition. Mol. Cell. Proteomics 5: 144-56.
188. Smith, R.D. and Anderson, G.A. (2002). An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2: 513-23.
189. Spence, G.M., Graham, A.N., Mulholland, K., Maxwell, P., McAllister, I., Sloan, J.M., Armstrong, M.A., Campbell, F.C., et al. (2002). Vascular endothelial growth factor levels in serum and plasma following esophageal cancer resection-relationship to platelet count. Int. J. Biol. Markers 17: 119-24.
190. States, D.J., Omenn, G.S., Blackwell, T.W., Fermin, D., Eng, J., Speicher, D.W. and Hanash, S.M. (2006). Challenges in deriving high-confidence protein identification from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24: 333-8.
191. Steennd, H. and Mann, M. (2004). The ABC's (and XYZ's) of peptide sequencing. Nature Rev. Mol. Cell. Biol. 5: 699-711.
192. Streckfus, C., Bigler, L., Tucci, M. and Thigpen, J.T. (2000). A preliminary study of CA 15-3, c-erbB-2, epidermal growth factor receptor, cathepsin-D, and p53 in saliva among women with breast carcinoma. Cancer Invest. 18: 101-9.
193. Sun, W., Li, F., Wu, S., Wang, X., Zheng, D., Wang, J. and Gao, Y. (2005). Human urine proteome analysis by three separation approaches. Proteomics 5: 4994-5001.
194. Tanaka, K., Waki, H., Ido, Y., Satoshi, A., Yoshida, Y., Yoshida, T., Matsuo, T. (1988). Protein and polymer analyses up to m/z 100000 by laser ionization time-of-flight mass spectrometry. Rapid. Commun. Mass Spectrom. 2: 151-3.
195. Tang, N., Tornatore, P. and Weinberger, S.R. (2004). Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23: 34-44.
196. Terry, D.E. and Desiderio, D.M. (2003). Between-gel reproducibility of the human cerebrospinal fluid proteome. Proteomics 3: 1962-79.
197. Theodorescu, D., Fliser, D., Wittke, S., Mischak, H., Krebs, R., Walden, M., Ross, M., Eltze, E., et al. (2006a). Pilot study of capillary electrophoresis coupled to mass spectrometry is a tool to define potential prostate cancer biomarkers in urine. Electrophoresis 26: 2792-808.
198. Theodorescu, D. and Mischak, H. (2007). Mass spectrometry based proteomics in urine biomarker discovery. World J. Urol. 25: 435-43.
199. Theodorescu, D., Wittke, S., Ross, M.M., Walden, M., Conway, M., Just, I., Mischak, H. and Frierson, H.F. (2006b). Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol. 7: 230-40.
200. Thongboonkerd, V. (2007). Recent progress in urinary proteomics. Proteomics Clin. Appl. 1: 780-91.
201. Thouvenot, E., Lafon-Cazal, M., Demettre, E., Jouin, P., Bockaert, J. and Marin, P. (2006). The proteome analysis of mouse choroids plexes secretome reveals a high protein secretion capacity of choroidal epithelial cells., Proteomics 6: 5941-52.
202. Traum, A.Z., Wells, M.P., Aivado, M., Libermann, T.A., Ramoni, M.F. and Schachter, A.D. (2006). SELDI-TOF MS of quadruplicative urine and serum samples to evaluate changes related to storage conditions. Proteomics 6: 1676-80.
203. Trojer, L., Stecher, I., Feurestein, I. and Bonn, G.K. (2005). Cu(II)-loaded iminodiacetic acid-silica peptides for protein profiling of human serum samples using surface-enhanced affinity capture support porosity effects. Rapid Commun. Mass Spectrom. 19: 3398-404.
204. Tryggvason, K. and Pettersson, E. (2003). Causes and consequences of proteinuria: the kidney filtration barrier and progressive renal failure. J. Intern. Med. 254: 216-24.
205. Tubb, D.L., Friedman, D.B. and Ham, A-J.L. (2006). Verification of automated peptide identification from proteomic tandem mass spectra. Nature Protocols 1: 2213-22.
206. Uhlén, M., Björling, E., Agaton, C., Szigyarto, C.A. Amini, B., Andersen, E., Andersson, A.C., Angelidou, P., et al. (2005). A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 4: 1920-32.
207. Urfer, W., Grzegorczyk, M. and Jung, K. (2006). Statistics for proteomics: a review of tools for analyzing experimental data. Proteomics 6 (Suppl. 2): 48-55.
208. Valmu, L., Paju, A., Lempinen, M., Kemppainen, E. and Stenman, U.H. (2006). Application of proteomic technology in identifying pancreatic secretory trypsin inhibitor variants in urine of patients with pancreatitis. Clin. Chem. 52: 73-81.
209. Van Dalen, A., Barak, V., Cremaschi, A., Gion, M., Molina, R., Namer, M., Stieber, P., Sturgeon, C., et al. (1998). The prognostic significance of increasing marker levels in metastatic breast cancer patients with clinically complete remission, partial remission or stable disease. Int. J. Biol. Markers 13: 10-5.
210. van der Helm, H.J. and Hische, E.A. (1979). Application of Baye's theorem to results of quantitative clinical chemical determinations. Clin. Chem. 25: 985-8.
211. van der Merme, D-E., Oikonomopoulou, K., Marshall, J. and Diamandis, E.P. (2007). Mass spectrometry: uncovering the cancer proteome for diagnostics. Adv. Cancer Res. 96: 23-50.
212. van Rhijin, B.W., van der Poel, H.G. and van der Kwast, T.H. (2005). Urine markers for bladder cancer surveillance: a systematic review. Eur. Urol. 47: 736-48.
213. Vercoutter-Edouart, A.S., Czeszak, X., Crepin, M., Lemoine, J., Bailly, B., Le Bourhis, X., Peyrat, J.P. and Hondermarck, H. (2004). Proteomic detection of changes in protein synthesis induced by fibroblast growth factor-2 in MCF-7 human breast cancer cells. Exp. Cell. Res. 262: 59-68.
214. Vestergaard, P. and Leverett, R. (1958) Constancy of urinary creatinine excretion. J. Lab. Clin. Med. 51: 211-8.
215. Villanueva, J., Shaffer, D.R., Philip, J., Chaparro, C.A., Erdjument-Bromage, H., Olshen, A.B., Fleisher, M., Lilja, H., et al. (2006). Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest. 116: 271-84.
216. Vitzthum, F., Behrens, F., Anderson, N.L. and Shaw, J.H. (2005). Proteomics: from basic research to diagnostic application. A review of requirements & needs. J. Proteome Res. 4: 1086-97.
217. Vlahou, A., Schellhammer, P.F., Mendrinos, S., Patel, K., Kondylis, F.L., Gong, L., Nasim, S., Wright, G.L. Jr. (2001). Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder. Am. J. Pathol. 158: 1491-502.
218. Vordenwülbecke, S.C.S., Weiberger, S.R. and Wiesner, A. (2005). Protein quantification by the SELDI-TOF-MS-based Protein Chip® System. Nat. Methods 2: 393-5.
219. Voshol, H., Brendlen, N., Muller, D., Inveradi, B., Augustin, A., Pally, C., Wieczorek, G., Morris, R.E., et al. (2005). Evaluation of biomarkers discovery approach to detect protein biomarkers of acute renal allograft rejection. J. Proteome Res. 4: 1192-9.
220. Voskoglou-Nomikos, T., Paler, J.L. and Seymour, L. (2003). Clinical predictive value of the in vitro cell line, human xenograft, and mouse allograft preclinical cancer models. Clin. Cancer Res. 9: 4227-39.
221. Wang, Y., Nacson, S. and Pawliszyn, J. (2007). The complexity of solid-phase microextraction/ surface enhanced laser desorption to ion mobility spectrometry for drug analysis. Anal. Chimica. Acta 582: 50-4.
222. Weissinger, E.M., Wittke, S., Kaiser, T., Haller, H., Bartel, S., Krebs, R., Golovko, I., Rupprecht, H.D. et al. (2004). Proteomic patterns established with capillary electrophoresis mass spectrometry for diagnostic purposes. Kidney Int. 65: 2426-34.
223. Welsh, J.B., Sapinoso, L.M., Kern, S.G., Brown, A.D., Liu, T., Bauskin, A.R., Ward, R.L., Hawkins, N.J., et al. (2003). Large-scale delineation of secreted protein biomarkers overexpressed in cancer tissue and serum. Proc. Natl. Acad. Sci. USA 100: 3410-5.
224. Wen, X., Dagan, S. and Wysocki, V.H. (2007). Small-molecule analysis with silicon-nanoparticle-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 79: 434-44.
225. West-Nørager, M., Kelstrup, C.D., Schou, C., Høgdall, E.V., Høgdall, C.K.
226. and Heegaard, N.H. (2007). Unravelling in vitro variables of major importance for the outcome of mass spectrometry-based serum proteomics. J. Chromatogr. B. 847: 30-7.
227. Wheeler, A.R., Moon, H., Bird, C.A., Loo, R.R., Kim, C.J., Loo, J.A. and Gavrell, R.L. (2005). Digital microfluidics with in-line sample purification for proteomic analysis with MALDI-MS. Anal. Chem. 77: 534-40.
228. Whitehouse, C.M., Dreyer, R.N., Yamashita, M. and Fenn, J.B. (1985). Electrospray interface for liquid chromatography and mass spectrometry. Anal. Chem. 57: 675-9.
229. Wilkins, M.R., Sanchez, J.-C., Cooley, A.A., Apple, K.D., Humphrey-Smith, I., Hochstrasser, D.F. and Williams, K.L. (1995). Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotech. Gen. Eng. Rev. 13: 19-50.
230. Wilkins, M.R. and Williams, K.L. (1997). Cross-species protein identification using amino acid composition, peptide mass finferprinting, isoelectric point and molecular mass in theoretical evaluation. J. Theor. Biol. 186: 7-15.
231. Wittke, S., Fliser, D., Haubitz, M., Bartel, S., Krebs, R., Hausadel, F., Hillmann, M., Golovko, I., et al. (2003). Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, as valuable tool for the establishment of new diagnostic markers. J. Chromatogr. A. 1013: 173-81.
232. Wittke, S., Mischak, H., Walden, M., Kolch, W., Rädler, T. and Wiedemann, K. (2005). Discovery of biomarkers in human urine and cerebrospinal fluid by capillary electrophoresis coupled to spectrometry: towards new diagnostic and therapeutic approach. Electrophoresis 26: 1476-87.
233. Woroniecki, R.P., Orlova, T.N., Mendelev, N., Shatat, I.F., Hailpern, S.M., Kaskel, F.P., Goligorsky, M.S. and O'Riordan, E. (2006). Urinary proteome of steroid-sensitive and steroid-resistant idiopathic nephritic syndrome of childhood. Am. J. Nephrol. 26: 258-67.
234. Xiao, Z., Prieto, D., Conrads, T.P., Veenstra, T.D. and Issaq, H.J. (2005). Proteomic patterns: their potential for disease diagnosis. Mol. Cell. Endocrinol. 230: 95-106.
235. Ye, B., Skates, S., Mok, S.C., Horick, N.K., Rosenberg, H.F., Vitonis, A., Edward, D., Sluss, P., et al. (2006). Proteome-based discovery and characterization of glycosylated eosinophil-derived neurotoxin and COOH-terminal osteoponin fragments for ovarian cancer in urine. Clin. Cancer Res. 12: 432-41.
236. Yousef, G.M., Plymeris, M.E., Yacoub, G.M., Scorilas, A., Sossaipillai, A., Popalis, C., Fracchioli, S., Katsaros, D., et al. (2003). Parallel overexpression of seven kallikerin genes in ovarian cancer. Cancer Res. 63: 2223-7.
237. Zerefos, P.G., Prados, J., Kossida, S., Kalousis, A. and Valhou, A. (2007). Sample preparation and bioinformatics in MALDI profiling of urinary proteins. J. Chromatogr. B. 853: 20-30.
238. Zerefos, P.G. and Valhou, A. (2008). Urine sample preparation and protein profiling by two-dimensional electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectrometry. Methods Mol. Biol. 428: 141-57.
239. Zhang, H., Liu, A.Y., Loriaux, P., Wollscheid, B., Zhou, Y., Watts, J.D. and Aebersold, R. (2007). Mass spectrometric detection of tissue proteins in plasma. Mol. Cell. Proteomics 6: 64-71.
240. Zhang, Z., Bast, R.C.Jr., Li, J., Sokoll, L.J., Rai, A.J., Rosenzweig, J.M., Cameron, B., Wang, Y.Y., et al. (2004). Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res. 64: 5882-90.
241. Zheng, Y., Li, H., Guo, Z., Lin, J.-M. and Cai, Z. (2007). Chip-based CE coupled to quadraupole TOF mass spectrometry for the analysis of glycopeptides. Electrophoresis 28: 1305-11.
242. Zhou, H., Yuen, P.S., Pisitkun, T., Gonzales, P.A., Yasuda, H., Dear, J.W., Gross, P., Knepper, M.A., et al. (2006). Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int. 69: 1471-6.
243. Zhou, M. and Veenstra, T.D. (2008). Mass spectrometry: m/z 1983-2008. BioTechniques 44: 667-70.
244. Zolg, W. (2006). The proteomic search for diagnostic biomarkers. Mol. Cell. Proteomics 5: 1720-6.
245. Zürbig, P., Renfrow, M.B., Schiffer, E., Novak, J., Walden, M., Wittke, S., Just, I., Pelzing, M., et al. (2006). Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform -independent separation. Electrophoresis 27: 2111-25.