Affinity-Based Biosensors, Microarrays and Proteomics

Proteome Analysis: Interpreting the Genome

Volumn , Issue , 2004, Pages 243-285

  Nice, Edouard ^a,b   Catimel, Bruno ^a  

^a ROYAL MELBOURNE HOSPITAL   (Australia)

^b Walter and Eliza Hall Institute for Medical Research   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84904079519     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-044451024-2/50027-8     Document Type: Chapter

References (169)

1. Wilkins M.R., Sanchez J.C., Gooley A.A., Appel R.D., Humphery-Smith I., Hochstrasser D.F., Williams K.L. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Engng Res. 1996, 13:19-50.
2. Gygi S.P., Rist B., Aebersold R. Measuring gene expression by quantitative proteome analysis. Curr. Opin. Biotechnol. 2000, 11:396-401.
3. Patterson S. Proteomics: the industrialization of protein chemistry. Curr. Opin. Biotechnol. 2000, 11:413-418.
4. Chalmers M.J., Gaskell S.J. Advances in mass spectrometry for proteome analysis. Curr. Opin. Biotechnol. 2000, 11:384-390.
5. Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA 2000, 97:9390-9395.
6. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 3:242-247.
7. Griffin T.J., Aebersold R. Advances in proteome analysis by mass spectrometry. J. Biol. Chem. 2001, 276:45497-45500.
8. Hebestreit H.F. Proteomics: an holistic analysis of nature's proteins. Curr. Opin. Pharmacol. 2001, 1:513-520.
9. Santoni V., Molloy M., Rabilloud T. Membrane proteins and proteomics: un amour impossible. Electrophoresis 2001, 21:1054-1070.
10. Opitek G.J., Ramirez S.M., Jorgenson J.W., Moseley M.A. Comprehensive two-dimensional high-performance chromatography for the isolation of overexpressed proteins and proteome mapping. Anal. Biochem. 1998, 258:349-361.
11. Link A.J., Eng J., Schiltz D.M., Carmack E., Mize G.J., Morris D.R., Garvick B.M., Yates J.R. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 1999, 17:676-682.
12. Corthals G., Wasinger V.C., Hochstrasser D.F., Sanchez J.C. The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000, 2:1104-1115.
13. Richter R., Schulz-Knappe P., John H., Forssmann W.-G. Posttranslationally processed forms of the human chemokine HCC-1. Biochemistry 2000, 39:10799-10805.
14. Standker L., Braulke T., Mark S., Mostafavi H., Meyer M., Honing S., Gimenez-Gallego G., Forssmann W.G. Partial IGF affinity of circulating N- and C-terminal fragments of human insulin-like growth factor binding protein-4 (IGFBP-4) and the disulfide bonding pattern of the C-terminal IGFBP-4 domain. Biochemistry 2000, 39:5082-5088.
15. Taylor R.S., Wu C.C., Hays L.G., Eng J.K., Yates J.R., Howell K.E. Proteomic of rat liver golgi complex: minor proteins are identified through sequential fractionation. Electrophoresis 2000, 21:3441-3459.
16. Liepke C., Zucht H.D., Forssmann W.G., Standker L. Purification of novel peptide antibiotics from human milk. J. Chromatogr. B 2001, 752:369-377.
17. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M., Remor M., Hofert C., Schelder M., Brajenovic M., Ruffner H., Merino A., Klein K., Hudak M., Dickson D., Rudi T., Gnau V., Bauch A., Bastuck S., Huhse B., Leutwein C., Heurtier M.A., Copley R.R., Edelmann A., Querfurth E., Rybin V., Drewes G., Raida M., Bouwmeester T., Bork P., Seraphin B., Kuster B., Neubauer G., Superti-Furga G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
18. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K., Yang L., Wolting C., Donaldson I., Schandorff S., Shewnarane J., Vo M., Taggart J., Goudreault M., Muskat B., Alfarano C., Dewar D., Lin Z., Michalickova K., Willems A.R., Sassi H., Nielsen P.A., Rasmussen K.J., Andersen J.R., Johansen L.E., Hansen L.H., Jespersen H., Podtelejnikov A., Nielsen E., Crawford J., Poulsen V., Sorensen B.D., Matthiesen J., Hendrickson R.C., Gleeson F., Pawson T., Moran M.F., Durocher D., Mann M., Hogue C.W., Figeys D., Tyers M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415:180-183.
19. Kachman M.T., Wang H., Schwartz D.R., Cho K.R., Lubman D.M. A 2-D liquid separations/mass mapping method for interlysate comparison of ovarian cancers. Anal. Chem. 2002, 74:1779-1791.
20. Catimel B., Rothacker J., Nice E. The use of biosensors for microaffinity purification: an integrated approach to proteomics. J. Biochem. Biophys. Methods 2001, 49:289-312.
21. Cass A.E.G. Molecular Biology and Biotechnology 1995, 110-113. VCH, London. R.A. Meyers (Ed.).
22. Nice E.C., Catimel B. Instumental biosensors: new perspectives for the analysis of biomolecular interaction. Bioessays 1999, 21:339-352.
23. Rich R.L., Myszka D.G. Advances in surface plasmon resonance biosensor analysis. Curr. Opin. Biotechnol. 2000, 11:54-61.
24. Leatherbarrow R.J., Edwards P.R. Analysis of molecular recognition using optical biosensors. Curr. Opin. Chem. Biol. 1999, 3:544-547.
25. Baird C.L., Muszka D.G. Current and emerging commercial optical biosensors. J. Mol. Recogn. 2001, 14:261-268.
26. Malmqvist M. Biospecific interaction analysis using biosensor technology. Nature 1983, 361:186-187.
27. Davies R.D., Edwards P.R., Watts H.J., Lowe C.R., Buckle P.E., Yeung D., Kinning T.M., Pollard-Knight D.V. The resonant mirror: a tool for the study of biomolecular interactions. Tech. Protein Chem. V 1994, 285-292.
28. Catimel B., Domagala T., Nerrie N., Weinstock J., Abud H., Heath J.K., Nice E.C. Recent applications of instrumental biosensors for protein and peptide structure-function studies. Protein Pept. Lett. 1999, 6:319-340.
29. Stenberg E., Persson B., Roos H., Urbaniczki J. Quantitative determination of surface concentration of protein with surface plasmon resonance using radiolabeled proteins. J. Colloid Interface Sci. 1990, 43:513-526.
30. Edwards P.R., Lowe P.A., Leatherbarrow R.J. Ligand loading at the surface of an optical biosensor and its effect upon the kinetics of protein-protein interactions. J. Mol. Recogn. 1997, 10:128-134.
31. Wade J.D., Domagala T., Rothacker J., Catimel B., Nice E.C. Use of thiazoline-mediated ligation for site specific biotinylation of mouse EGF for biosensor immobilisation. Lett. Pept. Sci. 2002, 58:493-503.
32. Huber A., Demartis S., Neri D. The use of biosensor technology for the engineering of antibodies and enzymes. J. Mol. Recogn. 1999, 12:198-216.
33. Rich R.L., Myszka D.G. Survey of the 1999 surface plasmon resonance biosensor literature. J. Mol. Recogn. 2000, 13:388-407.
34. Rich R.L., Myszka D.G. Survey of the year 2000 commercial optical biosensor literature. J. Mol. Recogn. 2001, 14:273-294.
35. Nice E.C., Catimel B., Lackmann M., Stacker S., Runting A., Wilks A., Nicola N., Burgess A.W. Strategies for the identification and purification of orphan biomolecules. Lett. Pept. Sci. 1997, 4:107-120.
36. Bartley T.D., Hunt R.W., Welcher A.A., Boyle W.J., Parker V.P., Lindberg R.A., Lu H.S., Colombero A.M., Elliott R.L., Guthrie B.A., Holst P.L., Skrine J.D., Toso R.J., Zhang M., Fernandez E., Trail G., Varnum B., Yarden Y., Hunter T., Fox G.M. B61 is a ligand for the ECK receptor-protein tyrosine kinase. Nature 1994, 368:558-560.
37. Stitt T.N., Conn G., Gore M., Lai C., Bruno J., Radziejewski C., Mattsson K., Fisher J., Gies D.R., Jones P.F., Masiakowski P., Rian T.E., Tobkes N.J., Chen D.H., DiStefano P.S., Long G.L., Basilico C., Goldfarb M.P., Lemke G., Glass D.J., Yancopoulos G.D. The anticoagulation factor protein S and its relative, Gas6, are ligands for the Tyro 3/Axl family of receptor tyrosine kinases. Cell 1995, 80:661-670.
38. Lackmann M., Bucci T., Mann R.J., Kravets L.A., Viney E., Smith F., Moritz R.L., Carter W., Simpson R.J., Nicola N.A., Mackwell K., Nice E.C., Wilks A.F., Boyd A.W. Purification of a ligand for the EPH-like receptor HEK using a biosensor-based affinity detection approach. Proc. Natl Acad. Sci. USA 1996, 93:2523-2527.
39. Davis S., Aldrich T.H., Jones P.F., Acheson A., Compton D.L., Jain V., Ryan T.E., Bruno J., Radziejewski C., Maisonpierre P.C., Yancopoulos G.D. Isolation of angiopoietin-1, a ligand for the TIE2 receptor, by secretion-trap expression cloning. Cell 1996, 87:1161-1169.
40. Sakano S., Serizawa R., Inada T., Iwama A., Itoh A., Kato C., Shimizu Y., Shinkai F., Shimizu R., Kondo S., Ohno M., Suda T. Characterization of a ligand for receptor protein-tyrosine kinase HTK expressed in immature hematopoietic cells. Oncogene 1996, 13:813-822.
41. Fitz L.J., Morris J.C., Towler P., Long A., Burgess P., Greco R., Wang R.J., Gassaway R., Nickbarg E., Kovacic S., Ciarletta A., Giannotti J.A., Finnerty H., Zollner R., Beier D.R., Leak L.V., Turner K.J., Wood C. Characterisation of murine Flt4 ligand/VEGF-C. Oncogene 1997, 15:613-618.
42. Catimel B., Ritter G., Welt S., Old L.J., Cohen L., Nerrie M.A., White S.J., Heath J.K., Demediuk B., Domagala T., Lee F.T., Scott A.M., Tu G.F., Ji H., Moritz R.L., Simpson R.J., Burgess A.W., Nice E.C. Purification and characterization of a novel restricted antigen expressed by normal and transformed human colonic epithelium. J. Biol. Chem. 1996, 271:25664-25670.
43. Seok Y.J., Sondej M., Badawi P., Lewis M.S., Briggs M.C., Jaffe H., Peterkofsky A. High affinity binding and allosteric regulation of Escherichia coli glycogen phosphorylase by the histidine phosphocarrier protein, HPr. J. Biol. Chem. 1997, 272:26511-26521.
44. Catimel B., Nerrie M., Lee F.T., Scott A.M., Ritter G., Welt S., Old L.J., Cohen L., White S., Heath J.K., Hong J., Moritz R.L., Simpson R.J., Burgess A.W., Nice E.C. Kinetic analysis of the interaction between the monoclonal antibody A33 and its colonic epithelial antigen using an optical biosensor: a comparison of immobilization strategies. J. Chromatogr. A 1997, 776:15-30.
45. Moritz R.L., Ritter G., Catimel B., Cohen L.S., Welt S., Old L.J., Burgess A.W., Nice E.C., Simpson R.J. Sequencing strategies for the human A33 antigen, a novel surface glycoprotein of human gastrointestinal epithelium. J. Chromatogr. A 1997, 798:91-101.
46. Ritter G., Cohen L.S., Nice E.C., Catimel B., Burgess A.W., Moritz R.L., Ji H., Heath J.K., White S., Welt S., Old L.J., Simpson R.J. Characterisation of post-translational modifications of human A33 antigen, a novel palmitoylated surface glycoprotein of human gastrointestinal epithelium. Biochem. Biophys. Res. Commun. 1997, 236:682-686.
47. Krone J.R., Nelson R.W., Dogruel D., Williams P., Granzow R. BIA/MS interfacing biomolecular interaction analysis with mass spectrometry. Anal. Biochem. 1997, 244:124-132.
48. Hillenkamp F., Karas M., Beavis R.C., Chait B.T. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 1991, 63:193A-1203A.
49. Karas M., Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 1998, 60:2299-2301.
50. Jardine L. Electrospray ionization mass spectrometry of biomolecules. Nature 1990, 345:747-748.
51. Nedelkov D., Nelson R.W. Practical considerations in BIA/MS: optimising the biosensor-mass spectrometry interface. J. Mol. Recogn. 2000, 13:140-145.
52. Nelson R.W., Krone J.R. Surface plasmon resonance biomolecular interaction analysis mass spectrometry. 1. Chip based analysis. Anal. Chem. 1997, 69:4363-4368.
53. Nelson R.W., Krone J.R., Jansson Ö. Surface plasmon resonance biomolecular interaction analysis mass spectrometry. 2. Fiber optic-based analysis. Anal. Chem. 1997, 69:4369-4374.
54. Nelson R.W., Krone J.R. Advances in surface plasmon resonance biomolecular interaction analysis mass spectrometry (BIA/MS). J. Mol. Recogn. 1999, 12:77-93.
55. Nelson R.W., Jarvik J.W., Taillon B.E., Tubbs K.A. BIA/MS of epitope-tagged peptides directly from E. coli lysate: multiplex detection and protein identification at lowfemtomole to subfemtomole levels. Anal. Chem. 1999, 71:2858-2865.
56. Nelson R.W., Nedelkov D., Tubbs K.A. Biosensor chip mass spectrometry: a chip-based proteomics approach. Electrophoresis 2000, 21:1155-1163.
57. Nedelkov D., Rassly A., Nelson R.W. Multitoxin biosensor-mass spectrometry analysis: a new approach for rapid, real-time, sensitive analysis of staphylococcal toxins in food. Int. J. Food Microbiol. 2000, 60:1-13.
58. Nelson R.W., Nedelkov D., Tubbs K.A. Biomolecular interaction analysis mass spectrometry. BIA/MS can detect and characterize proteins in complex biological fluids at the low- to subfemtomole level. Anal. Chem. 2000, 72:404A-411A.
59. Nedelkov D., Nelson R.W. Exploring the limit of detection in biomolecular interaction analysis mass spectrometry (BIA/MS): detection of attomole amounts of native protein present in complex biological mixture. Anal. Chim. Acta 2000, 423:1-7.
60. Nedelkov D., Nelson R.W. Analysis of native proteins from biological fluids by biomolecular interaction analysis mass spectrometry (BIA/MS): exploring the limit of detection, identification of non-specific binding and detection of multi-protein complexes. Biosens. Bioelectron. 2001, 16:1071-1078.
61. Nedelkov D., Nelson R.W. Analysis of human urine protein biomarkers via biomolecular interaction analysis mass spectrometry. Am. J. Kidney Dis. 2001, 38:481-487.
62. Nedelkov D., Nelson R.W. Biomolecular interaction analysis mass spectrometry: a multiplexed proteomic approach. PharmaGenomics 2001, 28-33.
63. Nedelkov D., Nelson R.W. Delineation of in vivo assembled multiprotein complexes via biomolecular interaction analysis mass spectrometry. Proteomics 2001, 1:1441-1446.
64. Williams C. Biotechnology match making: screening orphan ligands and receptors. Curr. Opin. Biotechnol. 2000, 11:42-46.
65. Natsume T., Nakayama H., Jansson Ö., Isobe T., Takio K., Mikoshiba K. Combination of biomolecular interaction analysis and mass spectrometric amino acid sequencing. Anal. Chem. 2000, 72:4193-4198.
66. Natsume T., Nakayama H., Toshiaki I. BIA-MS-MS: biomolecular interaction analysis for functional proteomics. Trends Biochem. 2001, 19:528-533.
67. Sönksen C.P., Nordhoff E., Jansson Ö., Malmqvist M., Roepstorff P. Combining MALDI mass spectrometry and biomolecular interaction analysis using a biomolecular interaction analysis instrument. Anal. Chem. 1998, 70:2731-2736.
68. Fitz L., Cook S., Nickbarg E., Wang J.H., Wood C.R. Accelerating ligand identification. BIA J. 1998, 5:23-25.
69. Catimel B., Weinstock J., Nerrie M., Domagala T., Nice E.C. Micropreparative ligand fishing with a cuvette-based optical mirror resonance biosensor. J. Chromatogr. A 2000, 869:261-273.
70. Roepstorff P., Sönksen C.P. A powerful combination: BIAcore 3000 and MALDI-TOF. BIA J. 1999, 6:9-11.
71. Zhukov A., Suckau D., Buijs B. From isolation to identification. Using surface plasmon resonance-mass spectrometry in proteomics. Pharmagenomics 2002, 2:18-28.
72. Williams C., Addona T.A. The integration of SPR biosensors with mass spectrometry: possible application for proteome analysis. Trends Biotechnol. 2000, 18:45-48.
73. Cao B., Urban J., Vaisar T., Shen R.Y.W., Kahn M. Detecting and identifying active compounds from a combinatorial library using IAsys and electrospray mass spectrometry. Technol. Protein Sci. Chem. 1997, 8:177-184.
74. Lowe P.A., Tristan J.H., Clark A., Davies R.J., Edwards P.R., Kinning T., Yeung D. New approaches for the analysis of molecular recognition using the IAsys evanescent wave biosensor. J. Mol. Recogn. 1998, 11:194-199.
75. Ji H., Moritz R.L., Ritter G., Catimel B., Nice E.C., Heath J.K., White S., Welt S., Old L.J., Burgess A.W., Simpson R.J. Electrophoretic analysis of the novel antigen for the colon-specific monoclonal antibody A33. Electrophoresis 1997, 18:614-621.
76. Simpson R.J., Connolly L.M., Eddes J.S., Pereira J.J., Moritz R.L., Reid G.E. Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database. Electrophoresis 2000, 21:1707-1732.
77. Catimel B., Rotacker J., Nice E.C. Biosensors and proteomics. Life Sci. 2002, 14:24-30.
78. Hutchens T.W., Yip T.T. New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom. 1993, 7:576-580.
79. Merchant M., Weinberger S.R. Recent advancements in surface-enhanced laser desorption/ionisation-time of flight-mass spectrometry. Electrophoresis 2000, 21:1164-1167.
80. Fung E.T., Thulasiraman V., Weinberger S.R., Dalmaso E.A. Protein biochips for differential profiling. Curr. Opin. Biotechnol. 2001, 12:65-69.
81. Weinberger S.C., Dalmaso E.A., Fung E.T. Current achievement using ProteinChip Array technology. Curr. Opin. Chem. Biol. 2001, 6:86-91.
82. Emmert-Buck M.R., Bonner R.F., Smith P.D., Chuaqui R.F., Zhuang Z., Goldstein S.R., Weiss R.A., Liotta L.A. Laser capture microdissection. Science 1996, 274:998-1001.
83. Banks R.E., Dunn M.J., Forbes M.A., Stanley A., Pappin D., Naven T., Gough M., Harnden P., Selby P.J. The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis - preliminary findings. Electrophoresis 2000, 20:689-700.
84. von Eggeling F., Davies H., Lomas L., Fiedler W., Junker K., Claussen U., Ernst G. Tissue-specific microdissection coupled with ProteinChip array technologies: applications in cancer research. Biotechniques 2000, 29:1066-1070.
85. Simone N.L., Paweletz C.P., Charbonneau L., Petricoin E.F., Liotta L.A. Laser capture microdissection: beyond functional genomics to proteomics. Mol. Diagn. 2000, 5:301-307.
86. Paweletz C.P., Gillespie J.W., Ornstein D.K., Simone N.L., Brown M.R., Cole K.A., Wang O.H., Huang J., Hu N., Yip T.T., Rich W.E., Kohn E.C., Linehan W.M., Weber T., Taylor P., Emmert-Buck M.R., Liotta L.A., Petricoin E.F. Rapid protein display profiling of cancer progression directly from human tissue using a protein biochip. Drug. Dev. Res. 2000, 49:34-42.
87. Paweletz C.P., Liotta L.A., Petricoin E.F. New technologies for biomarker analysis of prostate cancer progression: laser capture microdissection and tissue proteomics. Urology 2001, 57:160-163.
88. Wellmann A., Wollscheid V., Lu H., Ma Z.L., Albers P., Schutze K., Rohde V., Behrens P., Dreschers S., Ko Y., Wernert N. Analysis of microdissected prostate tissue with ProteinChip arrays - a way to new insights into carcinogenis and to diagnostic tools. Int. J. Mol. Med. 2002, 9:341-437.
89. Emmert-Buck M.R., Gillespie J.W., Paweletz C.P., Ornstein D.K., Basrur V., Appella E., Wang Q.H., Huang J., Hu N., Taylor P., Petricoin E.F. An approach to proteomic analysis of human tumors. Mol. Carcinog. 2000, 27:158-165.
90. von Eggeling F., Junker K., Fiedler W., Wollscheid V., Durst M., Claussen U., Ernst G. Mass spectrometry meets chip technology: a new proteomic tool in cancer research?. Electrophoresis 2001, 22:2898-2902.
91. Wulfkuhle J.D., McLean K.C., Paweletz C.P., Sroi D.C., Trock B.J., Steeg P., Petricoin E.F. New approach to proteomic analysis of breast cancer. Proteomics 2001, 1:1205-1215.
92. Wright J.L., Cazares L.H., Leung S.M., Nasim S., Adam B.L., Yip T.T., Schellhammer P.F., Gong L., Vlahou A. ProteinChip surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate biomarker in complex protein mixtures. Prostate Cancer Prostatic Dis. 2000, 2:264-276.
93. Adams B.L., Davis J.W., Cazares L.H., Schellhammer P.F., Wright G.L. Identifying the signature of prostate cancer in seminal plasma by SELDI affinity mass spectrometry. Proc. Am. Assoc. Cancer Res. 2000, 41:564.
94. Watkins B., Szaro R., Ball S., Knubovets T., Briggman J., Hlavaty J.J., Kusinitz F., Stieg A., Wu Y.I. Detection of early-stage cancer by serum analysis. Am. Lab. 2001, 32-36.
95. Rosty C., Christa L., Kuzdzalk S., Baldwin W.M., Zahurak M.L., Carnot F., Chan D.W., Canto M., Lillemoe K.D., Cameron J.L., Yeao C.J., Hruban R.H., Goggins M. Identification of hepatocarcinoma-intestine-pancreas/pancreatitis associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res. 2002, 62:1868-1875.
96. Paweletz C.P., Trock B., Pennanen M., Tsangaris T., Magnant C., Liottaand L.A., Petricoin E.F. Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new marker to aid in the diagnosis of breast cancer. Dis. Markers 2001, 17:301-307.
97. Petricoin E.F., Adekani A.M., Hittr B.A., Levine P.J., Fusaro V.A., Steinberg S.M., Mills G.B., Simone C., Fishman D.A., Kohn E.C., Liotta L.A. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359:572-577.
98. Ball G., Mian S., Holding F., Allibone R.O., Lowe J., Ali S., Li G., McCardle S., Ellis I.O., Creaser C., Rees R.C. An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumors and rapid identification of potential biomarkers. Bioinformatics 2002, 18:395-404.
99. Xiao Z., Beckett M.L., Wright G.L. Generation of a bacculovirus recombinant prostate-specific membrane antigen and its use in the development of a novel protein biochip quantitative imunoassay. Protein Exp. Purif. 2000, 19:12-21.
100. Xiao Z., Adam B.L., Cazares L.H., Clements M.A., Davis J.W., Schellhammer P.F., Dalmasso E.A., Wright G.L. Quantitation of serum prostate-specific membrane antigen by a novel protein biochip immunoassay discriminates benign from malignant prostate disease. Cancer Res. 2001, 61:6029-6033.
101. Davies H., Lomas L., Austen B. Profiling of amyloid beta peptide variants using SELDI Protein chip arrays. Biotechniques 1999, 27:1258-1261.
102. Austen B.M., Frears E.R., Davies H. The use of SELDI proteinchip arrays to monitor production of Alzheimer's betaamyloid in transfected cells. J. Pept. Sci. 2000, 6:459-469.
103. Lichtenthaler S.F., Beher D., Grimm H.S., Wang R., Shearman M.S., Masters C.L., Beyreuther K. The intramembrane cleavage site of the amyloid precursor protein depends on the length of its transmembrane domain. Proc. Natl Acad. Sci. USA 2002, 99:1365-1370.
104. Diamond D.L., Kimball J.R., Krisanaprakornkit S., Ganz T., Dale B.A. Detection of beta-defensins secreted by human oral epithelial cells. J. Immunol. Methods 2001, 256:65-76.
105. Tassi E., Al-Attar A., Aigner A., Swift M.R., McDonnell K., Karavanov A., Wellstein A. Enhancement of fibroblast growth factor (FGF) activity by an FGF-binding protein. J. Biol. Chem. 2001, 276:40247-40253.
106. Schenone M.M., Warder S.E., Martin J.A., Prorok M., Castellino F.J. An internal histidine residue from the bacterial surface protein, PAM, mediates its binding to the kringle-2 domain of human plasminogen. J. Pept. Res. 2000, 56:438-445.
107. Stoica G.E., Kuo A., Aigner A., Sunitha I., Souttou B., Malerczyk C., Caughey D.J., Wen D., Karavanov A., Riegel A.T., Wellstein A. Identification of anaplastic lymphoma kinase as a receptor for the growth factor pleiotrophin. J. Biol. Chem. 2001, 276:16772-16779.
108. Amaar Y.G., Thompson G.R., Linkhart T.A., Chen S.T., Baylink D.J., Mohan S. Insulin-like growth factor-binding protein 5 (IGFBP-5) interacts with a four and a half LIM protein 2 (FHL2). J. Biol. Chem. 2002, 277:12053-12060.
109. Steyn A.J., Collins D.M., Hondalus M.K., Jacobs W.R., Kawakami R.P., Bloom B.R. Mycobacterium tuberculosis WhiB3 interacts with RpoV to affect host survival but is dispensable for in vivo growth. Proc. Natl Acad. Sci. USA 2002, 99:3147-3152.
110. Adilakshmi T., Laine R.O. Ribosomal protein S25 mRNA partners with MTF-1 and La to provide a p53-mediated mechanism for survival or death. J. Biol. Chem. 2002, 277:4147-4151.
111. Forde C.E., Gonzales A.D., Smessaert J.M., Murphy G.A., Shields S.J., Fitch J.P., McCutchen-Maloney S.L. A rapid method to capture and screen for transcription factors by SELDI mass spectrometry. Biochem. Biophys. Res. Commun. 2002, 290:1328-1335.
112. Issaq H.J., Veenstra T.D., Conrads T.P., Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem. Biophys. Res. Commun. 2002, 292:587-592.
113. Spencer D.I., Robson L., Purdy D., Whitelegg N.R., Michael N.P., Bhatia J., Sharma S.K., Rees A.R., Minton N.P., Begentm R.H., Chester K.A. A strategy for mapping and neutralizing conformational immunogenic sites on protein therapeutics. Proteomics 2002, 2:271-279.
114. Walter G., Bussov K., Cagill D., Lueking A., Lerach H. Protein arrays for gene expression and molecular interaction screening. Curr. Opin. Biotechnol. 2000, 3:298-302.
115. Cahill D.J. Protein arrays: a high-throughput solution for proteome research?. Proteomics: A Trends Guide 2000, 47-51.
116. Emili A.Q., Cagney G. Large-scale functional protein analysis using peptide or protein arrays. Nat. Biotechnol. 2000, 18:393-397.
117. Zhu H., Snyder M. Protein chip technology. Curr. Opin. Chem. Biol. 2003, 7:55-63.
118. Templin M.F., Stoll D., Schrenk M., Traub P.C., Vohringer C.F., Joos T.O. Protein microarray technology. Trends Biotechnol. 2002, 20:160-166.
119. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S., Rothberg J.M. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
120. MacBeath G., Schreiber S.L. Printing proteins as microarrays for high-throughput function determination. Science 2000, 289:1760-1763.
121. Kodakek T. Protein microarrays: prospect and problems. Chem. Biol. 2001, 8:105-115.
122. Macbeath G. Proteomics come to the surface. Science 2001, 19:828-829.
123. Borrebaek C.A.K. Antibodies in diagnostics - from immunoassays to protein chips. Immunol. Today 2000, 8:379-382.
124. Goldmann R.D. Antibodies: indispensable tools for biomedical research. Trends Biochem. Sci. 2000, 25:593-595.
125. Gunneriusson E., Nord K., Uhlén M., Nygren P.A. Affinity maturation of a Taq DNA polymerase specific affibody by helix shuffling. Protein Engng 1999, 12:873-878.
126. Gunneriusson E., Samuelson P., Ringdahl J., Grönlund H., Nygren P.A., Stahl S. Staphylococcal surface-display of immunoglobulin A (IgA) and IgE specific in vitro-selected binding proteins (affibodies) based on Staphylococcus aureus protein A. Appl. Environ. Microbiol. 1999, 65:4134-4140.
127. Brody E.N., Willis M.C., Smith J.D., Jayasena S., Zichi D., Gold L. The use of aptamers in large arrays for molecular diagnostics. Mol. Diagn. 1999, 4:381-388.
128. Green L.S., Bell C., Janjic N. Aptamers as reagents for high-throughput screening. Biotechniques 2001, 30:1094-1096.
129. Houseman B.T., Huh J.H., Kron S.J., Mrksich M. Peptide chips for the quantitative evaluation of protein kinase activity. Nat. Biotechnol. 2002, 20:270-274.
130. Haupt K., Mosbach K. Plastic antibodies: developments and application. Trends Biotechnol. 1998, 16:468-479.
131. Vlatakis G., Andersson L.I., Muller R., Mosbach K. Drug assay using antibody mimics made by molecular imprinting. Nature 1993, 361:645-647.
132. Mendoza L.G., McQuary P., Mongan A., Gangadharan R., Brignac S., Eggers M. High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). BioTechniques 1999, 27:778-788.
133. Rowe C.A., Tender L.M., Feldstein M.J., Golden J.P., Scruggs S.B., Macgraith B.D., Cras J.J., Ligler F.S. Array biosensor for simultaneous identification of bacterial, viral and protein analyte. Anal. Chem. 1999, 71:3846-3852.
134. Arenkov P., Kukhtin A., Gemmell A., Voloshchuk S., Chupeeva V., Mirzabekov A. Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 2000, 278:123-131.
135. Wiese R., Belosludtev Y., Powdrill T., Thompson P., Hogan M. Simultaneous multianalyte ELISA on microarray platform. Clin. Chem. 2001, 47:1451-1457.
136. Schweitzer B., Roberts S., Grimwade B., Shao W., Wang M., Fu Q., Shu Q., Laroche I., Zhou Z., Tchernev V.T., Christiansen J., Velleca M., Kingsmore F. Multipexed protein profiling on microassays by rolling-circle amplification. Proc. Natl. Acad. Sci. USA 2000, 97:10113-10119.
137. Tam S.W., Wiese R., Lee S., Gilmore J., Kumble K.D. Simultaneous analysis of eight human Th1/Th2 cytokines using microarrays. J. Immunol. Methods 2000, 161:157-165.
138. Haab B.B., Dunham M.J., Brown P.O. Protein microarrays for highly parallel detection and quantification of proteins and antibodies in complex solutions. Genome Biol. 2001, 2:1-13.
139. Robinson W.H., DiGennaro C., Hueber W., Haab B.B., Kamachi M., Dean E.J., Fournel S., Fong D., Genovese M.C., de Vegvar H.E., Skriner K., Hirschberg D.L., Morris R.I., Muller S., Pruijn G.J., van Venrooij W.J., Smolen J.S., Brown P.O., Steinman L., Utz P.J. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nature Med. 2002, 8:295-301.
140. Silzel J.W., Cercek B., Dodson C., Tsai T., Obremski R.J. Mass-sensing, multianalyte microarray immunoassay with imaging detection. Clin. Chem. 1998, 44:2636-2643.
141. Mooney J.F., Hunt A.J., McIntosh J.R., Liberko C.A., Walba D.M., Rogers C.T. Patterning of functional antibodies and other proteins by photolithography of silane monolayers. Proc. Natl Acad. Sci. USA 1996, 93:12287-12291.
142. Jones W.W., Kenseth J.R., Porte M.D., Mosher C.L., Henderson E. Microminiaturized immunoassays using atomic force microscopy and compositionally patterned antigen arrays. Anal. Chem. 1998, 70:1233-1241.
143. Michael K.L., Taylor L.C., Schultz S.L., Walt D.R. Randomly ordered addressable high-density optical sensor arrays. Anal. Chem. 1998, 70:1242-1248.
144. Martin B.D., Gaber B.P., Patterson C.H., Turner D.C. Direct protein microarray fabrication using an hydrogel stamper. Langmuir 1998, 14:3971-3975.
145. Lueking A., Horn M., Eickhoff H., Bussov K., Lehrach H., Walter G. Protein microarrays for gene expression and antibody screening. Anal. Biochem. 1999, 170:103-111.
146. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-550.
147. Body E.N., Gold L. Aptamers as therapeutic and diagnostics agents. J. Biotechnol. 2000, 74:5-13.
148. Geysen H.M., Meloen R.H., Barteling S.J. Use of peptide synthesis to probe viral antigen for epitopes to a resolution of a single amino acid. Proc. Natl Acad USA 1984, 81:3998-4002.
149. Kramer A., Schneider-Mergener J. Synthesis and screening of peptide libraries on single resins and continuous cellulose membrane supports. Methods Mol. Biol. 1998, 87:25-39.
150. Kramer A., Reineke U., Dong L., Hoffmann B., Hoffmuller U., Winkler D., Volkmer-Engert R., Schneider-Mergener J. Spot synthesis: observations and optimizations. J. Pept. Res. 1999, 54:319-327.
151. Wenschuh H., Volkmer-Engert R., Schmidt M., Schulz M., Schneider-Mergener J., Reineke U. Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides. Biopolymers 2000, 55:188-206.
152. Kramer A., Volkmer-Engert R., Malin R., Reinekeand U., Schneider-Mergener J. Simultaneous examples for the identification of protein, metal and DNA binding peptide mixtures. Synthesis of peptide libraries on single resin and continuous cellulose membrane supports: examples for the identification of protein, metal and DNA binding peptide mixtures. Pept. Res. 1993, 6:314-319.
153. Reineke U., Volkmer-Engert R., Scheider-Mergener J. Applications of peptide arrays prepared by the spot technology. Curr. Opin. Biotechnol. 2001, 12:59-64.
154. deWildt R.M.T., Mundy C.R., Gorick B.D., Tomlinson I.M. Antibody arrays for highthroughput screening of antibody-antigen interactions. Nat. Biotechnol. 2000, 18:989-994.
155. Bussov K., Cahill D., Nietfeld W., Banvroft D., Scherzinger E., Lehrach H., Walter G. A method for global protein expression and antibody screening on high-density filter of an array cDNA library. Nucleic Acids Res. 1998, 26:5007-5008.
156. Kononen J., Bubendorf L., Kallioniemi A., Barlund M., Schraml P., Leighton S., Torhorst J., Mihatsch M.J., Sauter G., Kallioniemi O.P. Tissue microarrays for highthroughput molecular profiling of tumor specimen. Nat. Med. 1998, 4:844-847.
157. Barlund M., Forozan F., Kononen J., Bubendorf L., Chen Y., Bittner M.L., Torhorst J., Haas P., Bucher C., Sauter G., Kallioniemi O.P., Kallioniemi A. Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J. Clin. Oncol. 2002, 15:2417-2428.
158. Hoos A. Tissue microarray profiling of cancer specimens and cell lines: opportunities and limitations. Lab. Invest. 2001, 81:1331-1338.
159. Wang H., Wang H., Zhang W., Fuller G.N. Tissue microarrays: applications in neuropathology research, diagnosis, and education. Brain Pathol. 2002, 12:95-107.
160. Terris B., Bralet M.P. Tissue microarrays, or the advent of chips in pathology. Ann. Pathol. 2002, 69-72.
161. Hughes K., Lucas D., Stolowitz M., Wiley J. Novel affinity tools for protein immobilisation. Implications for proteomics. Am. Biotechnol. Lab. 2001, 1:36-38.
162. Stolowitz M., Ahlem C., Hughes K., Kaiser R., Kesicki E., Li G., Lund K., Torkelson S., Wiley J. Phenyldiboronic acid-salicylhydroxamic acid bioconjugates I: a novel boronic complex for protein immobilisation. Bioconjug. Chem. 2001, 12:229-239.
163. Martzen M.R., McCraith S.M., Spinelli S.L., Torres F.M., Fields S., Grayhack E.J., Phizicky E.M. A biochemical genomics approach for identifying genes by the activity of their products. Science 1999, 286:1153-1155.
164. Zhu H., Klemic J.F., Chang S., Bertone P., Casamayor A., Klemic K.C., Smith D., Gerstein M., Reed M.A., Snyder M. Analysis of yeast protein kinases using protein chips. Nat. Genet. 2000, 26:283-289.
165. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Didlingmaier S., Houfek T., Mitchell T., Miller P., Dean R.A., Gerstein M., Snyder M. Global analysis of protein activities using proteome chips. Science 2001, 293:2101-2105.
166. Liotta L.A., Espina V., Mehta A.I., Calvert V., Rosenblatt K., Geho D., Munson P.J., Young L., Wulfkuhle J., Petricoin E.F. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 2003, 3:317-325.
167. Service R.F. Recruiting genes, proteins for a revolution in diagnostics. Science 2003, 300:236-239.
168. Tyers M., Mann M. From genomics to proteomics. Nature 2003, 422:193-197.
169. Cutler P. Protein arrays: the current state-of-the-art. Proteomics 2003, 3:3-18.