Protein microarrays: Catching the proteome

Mechanisms of Ageing and Development

Volumn 126, Issue 1, 2005, Pages 161-170

  Poetz, Oliver ^a   Schwenk, Jochen M ^a   Kramer, Stefan ^a   Stoll, Dieter ^a   Templin, Markus F ^a   Joos, Thomas O ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Parallelised assay; Protein microarray; Proteomics

Indexed keywords

ENZYME; PROTEIN; PROTEOME;

AUTOIMMUNITY; CATALYSIS; CONFERENCE PAPER; DNA MICROARRAY; ENZYME SUBSTRATE; HUMAN; IMMUNOASSAY; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN PROTEIN INTERACTION; PROTEOMICS; TECHNOLOGY;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEOME;

EID: 11144294044     PISSN: 00476374     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mad.2004.09.030     Document Type: Conference Paper

References (71)

1. Anon. Chipping forecast II Nat. Genet. 32 2002 461 552
2. C.A. Bandera, B. Ye, and S.C. Mok New technologies for the identification of markers for early detection of ovarian cancer Curr. Opin. Obstet. Gynecol. 15 2003 51 55
3. R. Bellisario, R.J. Colinas, and K.A. Pass Simultaneous measurement of antibodies to three HIV-1 antigens in newborn dried blood-spot specimens using a multiplexed microsphere-based immunoassay Early Hum. Dev. 64 2001 21 25
4. L. Belov, O. de la Vega, C.G. dos Remedios, S.P. Mulligan, and R.I. Christopherson Immunophenotyping of leukemias using a cluster of differentiation antibody microarray Cancer Res. 61 2001 4483 4489
5. L. Belov, P. Huang, N. Barber, S.P. Mulligan, and R.I. Christopherson Identification of repertoires of surface antigens on leukemias using an antibody microarray Proteomics 3 2003 2147 2154
6. J.M. Boutell, D.J. Hart, B.L. Godber, R.Z. Kozlowski, and J.M. Blackburn Functional protein microarrays for parallel characterisation of p53 mutants Proteomics 4 2004 1950 1958
7. K. Bouwman, J. Qiu, H. Zhou, M. Schotanus, L.A. Mangold, R. Vogt, E. Erlandson, J. Trenkle, A.W. Partin, D. Misek, G.S. Omenn, B.B. Haab, and S. Hanash Microarrays of tumor cell derived proteins uncover a distinct pattern of prostate cancer serum immunoreactivity Proteomics 3 2003 2200 2207
8. L.L. Burns-Hamuro, Y. Ma, S. Kammerer, U. Reineke, C. Self, C. Cook, G.L. Olson, C.R. Cantor, A. Braun, and S.S. Taylor Designing isoform-specific peptide disruptors of protein kinase A localization Proc. Natl. Acad. Sci. USA 100 2003 4072 4077
9. E. Caputo, R. Moharram, and B.M. Martin Methods for on-chip protein analysis Anal. Biochem. 321 2003 116 124
10. R.T. Carson, and D.A. Vignali Simultaneous quantitation of 15 cytokines using a multiplexed flow cytometric assay J Immunol. Methods 227 1999 41 52
11. R. Chen, L. Lowe, J.D. Wilson, E. Crowther, K. Tzeggai, J.E. Bishop, and R. Varro Simultaneous quantification of six human cytokines in a single sample using microparticle-based flow cytometric technology Clin. Chem. 45 1999 1693 1694
12. G.G. Chung, M.P. Zerkowski, I.T. Ocal, M. Dolled-Filhart, J.Y. Kang, A. Psyrri, R.L. Camp, and D.L. Rimm Beta-Catenin and p53 analyses of a breast carcinoma tissue microarray Cancer 100 2004 2084 2092
13. W. De Jager, H. Te Velthuis, B.J. Prakken, W. Kuis, and G.T. Rijkers Simultaneous detection of 15 human cytokines in a single sample of stimulated peripheral blood mononuclear cells Clin. Diagn. Lab. Immunol. 10 2003 133 139
14. S.A. Dunbar, C.A. Vander Zee, K.G. Oliver, K.L. Karem, and J.W. Jacobson Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system J. Microbiol. Meth. 53 2003 245 252
15. R.P. Ekins Multi-analyte immunoassay J. Pharm. Biomed. Anal. 7 1989 155 168
16. A. Espejo, J. Cote, A. Bednarek, S. Richard, and M.T. Bedford A protein-domain microarray identifies novel protein-protein interactions Biochem. J. 367 2002 697 702
17. P. Finckh, H. Berger, J. Karl, U. Eichenlaub, K. Weindel, H. Hornauer, H. Lenz, P. Sluka, G.e. Weinreich, F. Chu, and R. Ekins Microspot - an ultrasensitive microarray-based ligand assay system. A practical application of ambient analyte assay theory Proc. UK NEQAS Meeting 3 1998 155 165
18. K. Freier, S. Joos, C. Flechtenmacher, F. Devens, A. Benner, F.X. Bosch, P. Lichter, and C. Hofele Tissue microarray analysis reveals site-specific prevalence of oncogene amplifications in head and neck squamous cell carcinoma Cancer Res. 63 2003 1179 1182
19. R.J. Fulton, R.L. McDade, P.L. Smith, L.J. Kienker, and J.R. Kettman Jr. Advanced multiplexed analysis with the FlowMetrix system Clin. Chem. 43 1997 1749 1756
20. A.C. Gavin, M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, C.M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M.A. Heurtier, R.R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147
21. H. Ge UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions Nucleic Acids Res. 28 2000 e3
22. D.N. Gosalia, and S.L. Diamond Printing chemical libraries on microarrays for fluid phase nanoliter reactions Proc. Natl. Acad. Sci. USA 100 2003 8721 8726
23. N. Grebenchtchikov, A. Brinkman, S.P. Van Broekhoven, D. De Jong, A. Geurts-Moespot, P.N. Span, H.A. Peters, H. Portengen, J.A. Foekens, C.G. Sweep, and L.C. Dorssers Development of an ELISA for measurement of BCAR1 protein in human breast cancer tissue Clin. Chem. 50 2004 1356 1363
24. R.L. Grubb, V.S. Calvert, J.D. Wulkuhle, C.P. Paweletz, W.M. Linehan, J.L. Phillips, R. Chuaqui, A. Valasco, J. Gillespie, M. Emmert-Buck, L.A. Liotta, and E.F. Petricoin Signal pathway profiling of prostate cancer using reverse phase protein arrays Proteomics 3 2003 2142 2146
25. S.P. Gygi, Y. Rochon, B.R. Franza, and R. Aebersold Correlation between protein and mRNA abundance in yeast Mol. Cell. Biol. 19 1999 1720 1730
26. Haab, B.B., Dunham, M.J., Brown, P.O., 2001. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2, RESEARCH0004.
27. B.T. Houseman, J.H. Huh, S.J. Kron, and M. Mrksich Peptide chips for the quantitative evaluation of protein kinase activity Nat. Biotechnol. 20 2002 270 274
28. S.S. Ivanov, A.S. Chung, P.Z. Yuan, A.Y. Guan, K.V. Sachs, J.S. Reichner, and Y.E. Chin Antibodies immobilized as arrays to profile protein post-translational modifications in mammalian cells Mol. Cell. Proteomics. 3 2004 788 795
29. M.B. Jones, H. Krutzsch, H. Shu, Y. Zhao, L.A. Liotta, E.C. Kohn, and E.F. Petricoin 3rd Proteomic analysis and identification of new biomarkers and therapeutic targets for invasive ovarian cancer Proteomics 2 2002 76 84
30. J.Y. Kang, M. Dolled-Filhart, I.T. Ocal, B. Singh, C.Y. Lin, R.B. Dickson, D.L. Rimm, and R.L. Camp Tissue microarray analysis of hepatocyte growth factor/Met pathway components reveals a role for Met, matriptase, and hepatocyte growth factor activator inhibitor 1 in the progression of node-negative breast cancer Cancer Res. 63 2003 1101 1105
31. V. Knezevic, C. Leethanakul, V.E. Bichsel, J.M. Worth, V.V. Prabhu, J.S. Gutkind, L.A. Liotta, P.J. Munson, E.F. Petricoin 3rd, and D.B. Krizman Proteomic profiling of the cancer microenvironment by antibody arrays Proteomics 1 2001 1271 1278
32. P.R. Knight, A. Sreekumar, J. Siddiqui, B. Laxman, S. Copeland, A. Chinnaiyan, and D.G. Remick Development of a sensitive microarray immunoassay and comparison with standard enzyme-linked immunoassay for cytokine analysis Shock 21 2004 26 30
33. J. Kononen, L. Bubendorf, A. Kallioniemi, M. Barlund, P. Schraml, S. Leighton, J. Torhorst, M.J. Mihatsch, G. Sauter, and O.P. Kallioniemi Tissue microarrays for high-throughput molecular profiling of tumor specimens Nat. Med. 4 1998 844 847
34. M.Y. Liu, S. Cai, A. Espejo, M.T. Bedford, and C.L. Walker 14-3-3 interacts with the tumor suppressor tuberin at Akt phosphorylation site(s) Cancer Res. 62 2002 6475 6480
35. J.M. Lizcano, M. Deak, N. Morrice, A. Kieloch, C.J. Hastie, L. Dong, M. Schutkowski, U. Reimer, and D.R. Alessi Molecular basis for the substrate specificity of NIMA-related kinase-6 (NEK6). Evidence that NEK6 does not phosphorylate the hydrophobic motif of ribosomal S6 protein kinase and serum- and glucocorticoid-induced protein kinase in vivo J. Biol. Chem. 277 2002 27839 27849
36. A. Lueking, A. Possling, O. Huber, A. Beveridge, M. Horn, H. Eickhoff, J. Schuchardt, H. Lehrach, and D.J. Cahill A nonredundant human protein chip for antibody screening and serum profiling Mol. Cell. Proteomics 2 2003 1342 1349
37. G. MacBeath Protein microarrays and proteomics Nat. Genet. 32 Suppl. 2002 526 532
38. G. MacBeath, A. Koehler, and S. Schreiber Printing small molecules as microarrays and detecting protein-ligand interactions en masse J. Am. Chem. Soc. 121 1999 7967 7968
39. K. Martin, T.H. Steinberg, L.A. Cooley, K.R. Gee, J.M. Beechem, and W.F. Patton Quantitative analysis of protein phosphorylation status and protein kinase activity on microarrays using a novel fluorescent phosphorylation sensor dye Proteomics 3 2003 1244 1255
40. M.T. McBride, S. Gammon, M. Pitesky, T.W. O'Brien, T. Smith, J. Aldrich, R.G. Langlois, B. Colston, and K.S. Venkateswaran Multiplexed liquid arrays for simultaneous detection of simulants of biological warfare agents Anal. Chem. 75 2003 1924 1930
41. M.T. McBride, D. Masquelier, B.J. Hindson, A.J. Makarewicz, S. Brown, K. Burris, T. Metz, R.G. Langlois, K.W. Tsang, R. Bryan, D.A. Anderson, K.S. Venkateswaran, F.P. Milanovich, and B.W. Colston Jr. Autonomous detection of aerosolized Bacillus anthracis and Yersinia pestis Anal. Chem. 75 2003 5293 5299
42. G.A. Michaud, M. Salcius, F. Zhou, R. Bangham, J. Bonin, H. Guo, M. Snyder, P.F. Predki, and B.I. Schweitzer Analyzing antibody specificity with whole proteome microarrays Nat. Biotechnol. 21 2003 1509 1512
43. M.J. Nam, J. Madoz-Gurpide, H. Wang, P. Lescure, C.E. Schmalbach, R. Zhao, D.E. Misek, R. Kuick, D.E. Brenner, and S.M. Hanash Molecular profiling of the immune response in colon cancer using protein microarrays: occurrence of autoantibodies to ubiquitin C-terminal hydrolase L3 Proteomics 3 2003 2108 2115
44. J.R. Newman, and A.E. Keating Comprehensive identification of human bZIP interactions with coiled-coil arrays Science 300 2003 2097 2101
45. U.B. Nielsen, M.H. Cardone, A.J. Sinskey, G. MacBeath, and P.K. Sorger Profiling receptor tyrosine kinase activation by using Ab microarrays Proc. Natl. Acad. Sci. USA 100 2003 9330 9335
46. S. Nishizuka, L. Charboneau, L. Young, S. Major, W.C. Reinhold, M. Waltham, H. Kouros-Mehr, K.J. Bussey, J.K. Lee, V. Espina, P.J. Munson, E. Petricoin 3rd, L.A. Liotta, and J.N. Weinstein Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays Proc. Natl. Acad. Sci. USA 100 2003 14229 14234
47. D. Opalka, C.E. Lachman, S.A. MacMullen, K.U. Jansen, J.F. Smith, N. Chirmule, and M.T. Esser Simultaneous quantitation of antibodies to neutralizing epitopes on virus-like particles for human papillomavirus types 6, 11, 16, and 18 by a multiplexed luminex assay Clin. Diagn. Lab. Immunol. 10 2003 108 115
48. D.K. Ornstein, J.W. Gillespie, C.P. Paweletz, P.H. Duray, J. Herring, C.D. Vocke, S.L. Topalian, D.G. Bostwick, W.M. Linehan, E.F. Petricoin 3rd, and M.R. Emmert-Buck Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines Electrophoresis 21 2000 2235 2242
49. A. Pandey, and M. Mann Proteomics to study genes and genomes Nature 405 2000 837 846
50. C.P. Paweletz, L. Charboneau, V.E. Bichsel, N.L. Simone, T. Chen, J.W. Gillespie, M.R. Emmert-Buck, M.J. Roth, I.E. Petricoin, and L.A. Liotta Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front Oncogene 20 2001 1981 1989
51. E. Petricoin, J. Wulfkuhle, V. Espina, and L.A. Liotta Clinical proteomics: revolutionizing disease detection and patient tailoring therapy J. Proteome Res. 3 2004 209 217
52. E.F. Petricoin, and L.A. Liotta Proteomic analysis at the bedside: early detection of cancer Trends Biotechnol. 20 2002 S30 S34
53. U. Prabhakar, E. Eirikis, and H.M. Davis Simultaneous quantification of proinflammatory cytokines in human plasma using the LabMAP assay J. Immunol. Methods 260 2002 207 218
54. U. Reineke, R. Volkmer-Engert, and J. Schneider-Mergener Applications of peptide arrays prepared by the SPOT-technology Curr. Opin. Biotechnol. 12 2001 59 64
55. G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 17 1999 1030 1032
56. G. Sauter, R. Simon, and K. Hillan Tissue microarrays in drug discovery Nat. Rev. Drug Discov. 2 2003 962 972
57. B. Schweitzer, S. Roberts, B. Grimwade, W. Shao, M. Wang, Q. Fu, Q. Shu, I. Laroche, Z. Zhou, V.T. Tchernev, J. Christiansen, M. Velleca, and S.F. Kingsmore Multiplexed protein profiling on microarrays by rolling-circle amplification Nat. Biotechnol. 20 2002 359 365
58. B. Schweitzer, S. Wiltshire, J. Lambert, S. O'Malley, K. Kukanskis, Z. Zhu, S.F. Kingsmore, P.M. Lizardi, and D.C. Ward Inaugural article: immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection Proc. Natl. Acad. Sci. USA 97 2000 10113 10119
59. W. Shao, Z. Zhou, I. Laroche, H. Lu, Q. Zong, D.D. Patel, S. Kingsmore, and S.P. Piccoli Optimization of rolling-circle amplified protein microarrays for multiplexed protein profiling J. Biomed. Biotechnol. 2003 299 307
60. Soen, Y., Chen, D.S., Kraft, D.L., Davis, M.M., Brown, P.O., 2003. Detection and characterization of cellular immune responses using peptide-MHC microarrays. PLoS Biol. 1, E65.
61. A. Sreekumar, M.K. Nyati, S. Varambally, T.R. Barrette, D. Ghosh, T.S. Lawrence, and A.M. Chinnaiyan Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins Cancer Res. 61 2001 7585 7593
62. N. Tang, P. Tornatore, and S.R. Weinberger Current developments in SELDI affinity technology Mass Spectrom. Rev. 23 2004 34 44
63. M.F. Templin, D. Stoll, J.M. Schwenk, O. Potz, S. Kramer, and T.O. Joos Protein microarrays: promising tools for proteomic research Proteomics 3 2003 2155 2166
64. T. Uchida, A. Fukawa, M. Uchida, K. Fujita, and K. Saito Application of a novel protein biochip technology for detection and identification of rheumatoid arthritis biomarkers in synovial fluid J. Proteome Res. 1 2002 495 499
65. P. Uetz, L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J.M. Rothberg A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 2000 623 627
66. Y. Wang Immunostaining with dissociable antibody microarrays Proteomics 4 2004 20 26
67. N. Winssinger, S. Ficarro, P.G. Schultz, and J.L. Harris Profiling protein function with small molecule microarrays Proc. Natl. Acad. Sci. USA 99 2002 11139 11144
68. F. Yan, A. Sreekumar, B. Laxman, A.M. Chinnaiyan, D.M. Lubman, and T.J. Barder Protein microarrays using liquid phase fractionation of cell lysates Proteomics 3 2003 1228 1235
69. L. Zhang, W. Yu, T. He, J. Yu, R.E. Caffrey, E.A. Dalmasso, S. Fu, T. Pham, J. Mei, J.J. Ho, W. Zhang, P. Lopez, and D.D. Ho Contribution of human alpha-defensin 1, 2, and 3 to the anti-HIV-1 activity of CD8 antiviral factor Science 298 2002 995 1000
70. H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R.A. Dean, M. Gerstein, and M. Snyder Global analysis of protein activities using proteome chips Science 293 2001 2101 2105
71. H. Zhu, J.F. Klemic, S. Chang, P. Bertone, A. Casamayor, K.G. Klemic, D. Smith, M. Gerstein, M.A. Reed, and M. Snyder Analysis of yeast protein kinases using protein chips Nat. Genet. 26 2000 283 289