Multiplex approaches in protein microarray technology

References

• Orchard S, Hermjakob H, Apweiler R. Annotating the human proteome. Mol. Cell. Proteomics 4(4), 435–440 (2005).
   PubMed Web of Science ®Google Scholar
• Laurell T, Marko-Varga G. Miniaturisation is mandatory unravelling the human proteome. Proteomics 2(4), 345–351 (2002).
   PubMed Web of Science ®Google Scholar
• McCarthy JE. Posttranscriptional control of gene expression in yeast. Microbiol. Mol. Biol. Rev. 62(4), 1492–1553 (1998).
   PubMed Web of Science ®Google Scholar
• Meri S, Baumann M. Proteomics: posttranslational modifications, immune responses and current analytical tools. Biomol. Eng. 18(5), 213–220 (2001).
   PubMedGoogle Scholar
• Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. Protein analysis on a proteomic scale. Nature 422(6928), 208–215 (2003).
   PubMed Web of Science ®Google Scholar
• Glokler J, Angenendt P. Protein and antibody microarray technology. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 797(1–2), 229–240 (2003).
   PubMed Web of Science ®Google Scholar
• Feilner T, Kreutzberger J, Niemann B et al. Proteomic studies using microarrays. Curr. Proteomics 1(4), 283–295 (2004).
   Google Scholar
• Labaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9(1), 14–19 (2005).
   PubMed Web of Science ®Google Scholar
• Zhu H, Snyder M. Protein chip technology. Curr. Opin. Chem. Biol. 7(1), 55–63 (2003).
   PubMed Web of Science ®Google Scholar
• Melton L. Protein arrays: proteomics in multiplex. Nature 429(6987), 101–107 (2004).
   PubMed Web of Science ®Google Scholar
• Hampel H, Goernitz A, Buerger K. Advances in the development of biomarkers for Alzheimer’s disease: from CSF total tau and Aβ1–42 proteins to phosphorylated tau protein. Brain Res. Bull. 61(3), 243–253 (2003).
   PubMed Web of Science ®Google Scholar
• MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science 289(5485), 1760–1763 (2000).
   PubMed Web of Science ®Google Scholar
• Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2(2), RESEARCH0004 (2001).
   PubMedGoogle Scholar
• Steinhauer C, Wingren C, Hager AC, Borrebaeck CA. Single framework recombinant antibody fragments designed for protein chip applications. Biotechniques (Suppl.) 38–45 (2002).
   PubMed Web of Science ®Google Scholar
• Lee M, Walt DR. A fiber-optic microarray biosensor using aptamers as receptors. Anal. Biochem. 282(1), 142–146 (2000).
   PubMed Web of Science ®Google Scholar
• Collett JR, Cho EJ, Lee JF et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal. Biochem. 338(1), 113–123 (2005).
   PubMed Web of Science ®Google Scholar
• Kodadek T, Reddy MM, Olivos HJ, Bachhawat-Sikder K, Alluri PG. Synthetic molecules as antibody replacements. Acc. Chem. Res. 37(9), 711–718 (2004).
   PubMed Web of Science ®Google Scholar
• Pellois JP, Zhou X, Srivannavit O, Zhou T, Gulari E, Gao X. Individually addressable parallel peptide synthesis on microchips. Nature Biotechnol. 20(9), 922–926 (2002).
   PubMed Web of Science ®Google Scholar
• Min DH, Mrksich M. Peptide arrays: towards routine implementation. Curr. Opin. Chem. Biol. 8(5), 554–558 (2004).
   PubMed Web of Science ®Google Scholar
• Paweletz CP, Charboneau L, Bichsel VE et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20(16), 1981–1989 (2001).
   PubMed Web of Science ®Google Scholar
• Ramachandran N, Hainsworth E, Bhullar B et al. Self-assembling protein microarrays. Science 305(5680), 86–90 (2004).
   PubMed Web of Science ®Google Scholar
• Büssow K, Cahill D, Nietfeld W et al. A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Res. 26(21), 5007–5008 (1998).
   PubMed Web of Science ®Google Scholar
• Holt LJ, Bussow K, Walter G, Tomlinson IM. Bypassing selection: direct screening for antibody–antigen interactions using protein arrays. Nucleic Acids Res. 28(15), E72 (2000).
   PubMed Web of Science ®Google Scholar
• Lueking A, Horn M, Eickhoff H, Bussow K, Lehrach H, Walter G. Protein microarrays for gene expression and antibody screening. Anal. Biochem. 270(1), 103–111 (1999).
   PubMed Web of Science ®Google Scholar
• Ge H. UPA, a universal protein array system for quantitative detection of protein–protein, protein–DNA, protein–RNA and protein–ligand interactions. Nucleic Acids Res. 28(2), e3 (2000).
   PubMedGoogle Scholar
• Snapyan M, Lecocq M, Guevel L, Arnaud MC, Ghochikyan A, Sakanyan V. Dissecting DNA–protein and protein–protein interactions involved in bacterial transcriptional regulation by a sensitive protein array method combining a near-infrared fluorescence detection. Proteomics 3(5), 647–657 (2003).
   PubMed Web of Science ®Google Scholar
• Angenendt P, Glökler J, Sobek J, Lehrach H, Cahill DJ. Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. J. Chromatogr. A 1009(1–2), 97–104 (2003).
   PubMed Web of Science ®Google Scholar
• Arenkov P, Kukhtin A, Gemmell A, Voloshchuk S, Chupeeva V, Mirzabekov A. Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 278(2), 123–131 (2000).
   PubMed Web of Science ®Google Scholar
• Kersten B, Feilner T, Kramer A et al. Generation of Arabidopsis protein chips for antibody and serum screening. Plant Mol. Biol. 52(5), 999–1010 (2003).
   PubMed Web of Science ®Google Scholar
• Angenendt P, Glökler J, Murphy D, Lehrach H, Cahill DJ. Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal. Biochem. 309(2), 253–260 (2002).
   PubMed Web of Science ®Google Scholar
• Afanassiev V, Hanemann V, Wolfl S. Preparation of DNA and protein micro arrays on glass slides coated with an agarose film. Nucleic Acids Res. 28(12), E66 (2000).
   PubMed Web of Science ®Google Scholar
• Kukar T, Eckenrode S, Gu Y et al. Protein microarrays to detect protein–protein interactions using red and green fluorescent proteins. Anal. Biochem. 306(1), 50–54 (2002).
   PubMed Web of Science ®Google Scholar
• Kramer A, Feilner T, Possling A et al. Identification of barley CK2α targets by using the protein microarray technology. Phytochemistry 65(12), 1777–1784 (2004).
   PubMed Web of Science ®Google Scholar
• Kersten B, Possling A, Blaesing F, Mirgorodskaya E, Gobom J, Seitz H. Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein–DNA interactions. Anal. Biochem. 331(2), 303–313 (2004).
   PubMed Web of Science ®Google Scholar
• Kiyonaka S, Sada K, Yoshimura I, Shinkai S, Kato N, Hamachi I. Semi-wet peptide/protein array using supramolecular hydrogel. Nature Mater. 3(1), 58–64 (2004).
   PubMed Web of Science ®Google Scholar
• Cretich M, Pirri G, Damin F, Solinas I, Chiari M. A new polymeric coating for protein microarrays. Anal. Biochem. 332(1), 67–74 (2004).
   PubMed Web of Science ®Google Scholar
• Kusnezow W, Jacob A, Walijew A, Diehl F, Hoheisel JD. Antibody microarrays: an evaluation of production parameters. Proteomics 3(3), 254–264 (2003).
   PubMed Web of Science ®Google Scholar
• Peluso P, Wilson DS, Do D et al. Optimizing antibody immobilization strategies for the construction of protein microarrays. Anal. Biochem. 312(2), 113–124 (2003).
   PubMed Web of Science ®Google Scholar
• Zhu H, Bilgin M, Bangham R et al. Global analysis of protein activities using proteome chips. Science 293(5537), 2101–2105 (2001).
   PubMed Web of Science ®Google Scholar
• Wingren C, Steinhauer C, Ingvarsson J, Persson E, Larsson K, Borrebaeck CA. Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complex proteomes. Proteomics 2424 (2005).
   PubMed Web of Science ®Google Scholar
• Weng S, Gu K, Hammond PW et al. Generating addressable protein microarrays with PROfusion covalent mRNA–protein fusion technology. Proteomics 2(1), 48–57 (2002).
   PubMed Web of Science ®Google Scholar
• Birkert O, Haake HM, Schutz A et al. A streptavidin surface on planar glass substrates for the detection of biomolecular interaction. Anal. Biochem. 282(2), 200–208 (2000).
   PubMed Web of Science ®Google Scholar
• Pavlickova P, Jensen NM, Paul H et al. Antibody detection in human serum using a versatile protein chip platform constructed by applying nanoscale self-assembled architectures on gold. J. Proteome Res. 1(3), 227–231 (2002).
   PubMed Web of Science ®Google Scholar
• Templin MF, Stoll D, Schwenk JM, Potz O, Kramer S, Joos TO. Protein microarrays: promising tools for proteomic research. Proteomics 3(11), 2155–2166 (2003).
   PubMed Web of Science ®Google Scholar
• Zhu H, Klemic JF, Chang S et al. Analysis of yeast protein kinases using protein chips. Nature Genet. 26(3), 283–289 (2000).
   PubMed Web of Science ®Google Scholar
• Borrebaeck CA, Ekstrom S, Hager AC, Nilsson J, Laurell T, Marko-Varga G. Protein chips based on recombinant antibody fragments: a highly sensitive approach as detected by mass spectrometry. Biotechniques 30(5), 1126–1130, 1132 (2001).
   PubMed Web of Science ®Google Scholar
• Haab BB. Advances in protein microarray technology for protein expression and interaction profiling. Curr. Opin. Drug Discov. Devel. 4(1), 116–123 (2001).
   PubMedGoogle Scholar
• Huang RP. Detection of multiple proteins in an antibody-based protein microarray system. J. Immunol. Methods 255(1–2), 1–13 (2001).
   PubMed Web of Science ®Google Scholar
• Schweitzer B, Roberts S, Grimwade B et al. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nature Biotechnol. 20(4), 359–365 (2002).
   PubMed Web of Science ®Google Scholar
• Kim TE, Park SW, Cho NY et al. Quantitative measurement of serum allergen-specific IgE on protein chip. Exp. Mol. Med. 34(2), 152–158 (2002).
   PubMed Web of Science ®Google Scholar
• Nelson BP, Liles MR, Frederick KB, Corn RM, Goodman RM. Label-free detection of 16S ribosomal RNA hybridization on reusable DNA arrays using surface plasmon resonance imaging. Environ. Microbiol. 4(11), 735–743 (2002).
   PubMed Web of Science ®Google Scholar
• Striebel HM, Schellenberg P, Grigaravicius P, Greulich KO. Readout of protein microarrays using intrinsic time resolved UV fluorescence for label-free detection. Proteomics 4(6), 1703–1711 (2004).
   PubMed Web of Science ®Google Scholar
• Dare TO, Davies HA, Turton JA, Lomas L, Williams TC, York MJ. Application of surface-enhanced laser desorption/ionization technology to the detection and identification of urinary parvalbumin-α: a biomarker of compound-induced skeletal muscle toxicity in the rat. Electrophoresis 23(18), 3241–3251 (2002).
   PubMed Web of Science ®Google Scholar
• Wang ZH, Jin G. A label-free multisensing immunosensor based on imaging ellipsometry. Anal. Chem. 75(22), 6119–6123 (2003).
   PubMed Web of Science ®Google Scholar
• Cheran LE, Chacko M, Zhang M, Thompson M. Protein microarray scanning in label-free format by Kelvin nanoprobe. Analyst 129(2), 161–168 (2004).
   PubMed Web of Science ®Google Scholar
• Shumaker-Parry JS, Zareie MH, Aebersold R, Campbell CT. Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein–DNA interactions by surface plasmon resonance microscopy. Anal. Chem. 76(4), 918–29 (2004).
   PubMed Web of Science ®Google Scholar
• Poetz O, Schwenk JM, Kramer S, Stoll D, Templin MF, Joos TO. Protein microarrays: catching the proteome. Mech. Ageing Dev. 126(1), 161–70 (2005).
   PubMed Web of Science ®Google Scholar
• Nielsen UB, Cardone MH, Sinskey AJ, MacBeath G, Sorger PK. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc. Natl Acad. Sci USA 100(16), 9330–9335 (2003).
   PubMed Web of Science ®Google Scholar
• Shao W, Zhou Z, Laroche I et al. Optimization of rolling-circle amplified protein microarrays for multiplexed protein profiling. J. Biomed. Biotechnol. 2003(5), 299–307 (2003).
   PubMedGoogle Scholar
• Robinson WH, DiGennaro C, Hueber W et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nature Med. 8(3), 295–301 (2002).
   PubMed Web of Science ®Google Scholar
• Nishizuka S, Charboneau L, Young L et al. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc. Natl Acad. Sci. USA 100(24), 14229–14234 (2003).
   PubMed Web of Science ®Google Scholar
• Qiu J, Madoz-Gurpide J, Misek DE et al. Development of natural protein microarrays for diagnosing cancer based on an antibody response to tumor antigens. J. Proteome Res. 3(2), 261–267 (2004).
   PubMed Web of Science ®Google Scholar
• Chan SM, Ermann J, Su L, Fathman CG, Utz PJ. Protein microarrays for multiplex analysis of signal transduction pathways. Nature Med. 10(12), 1390–1396 (2004).
   PubMed Web of Science ®Google Scholar
• Sydor JR, Nock S. Protein expression profiling arrays: tools for the multiplexed high-throughput analysis of proteins. Proteome Sci. 1(1), 3 (2003).
   PubMedGoogle Scholar
• Nielsen UB, Geierstanger BH. Multiplexed sandwich assays in microarray format. J. Immunol. Methods 290(1–2), 107–120 (2004).
   PubMed Web of Science ®Google Scholar
• Mendoza LG, McQuary P, Mongan A, Gangadharan R, Brignac S, Eggers M. High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques 27(4), 778–780 (1999).
   PubMed Web of Science ®Google Scholar
• Tam SW, Wiese R, Lee S, Gilmore J, Kumble KD. Simultaneous analysis of eight human Th1/Th2 cytokines using microarrays. J. Immunol. Methods 261(1–2), 157–165 (2002).
   PubMed Web of Science ®Google Scholar
• Shriver-Lake LC, Donner B, Edelstein R, Breslin K, Bhatia SK, Ligler FS. Antibody immobilization using heterobifunctional crosslinkers. Biosens. Bioelectron. 12(11), 1101–1106 (1997).
   PubMed Web of Science ®Google Scholar
• Angenendt P. Progress in protein and antibody microarray technology. Drug Discov. Today 10(7), 503–511 (2005).
   PubMed Web of Science ®Google Scholar
• Sreekumar A, Nyati MK, Varambally S et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 61(20), 7585–7593 (2001).
   PubMed Web of Science ®Google Scholar
• Miller JC, Zhou H, Kwekel J et al. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 3(1), 56–63 (2003).
   PubMed Web of Science ®Google Scholar
• Quackenbush J. Computational analysis of microarray data. Nature Rev. Genet. 2(6), 418–427 (2001).
   PubMed Web of Science ®Google Scholar
• Schweitzer B, Predki P, Snyder M. Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 3(11), 2190–2199 (2003).
   PubMed Web of Science ®Google Scholar
• Michaud GA, Salcius M, Zhou F et al. Analyzing antibody specificity with whole proteome microarrays. Nature Biotechnol. 21(12), 1509–1512 (2003).
   PubMed Web of Science ®Google Scholar
• Kim SH, Tamrazi A, Carlson KE, Katzenellenbogen JA. A proteomic microarray approach for exploring ligand-initiated nuclear hormone receptor pharmacology, receptor-selectivity,and heterodimer functionality. Mol. Cell. Proteomics 4(2), 267–277 (2004).
   PubMed Web of Science ®Google Scholar
• Biran I, Rissin DM, Ron EZ, Walt DR. Optical imaging fiber-based live bacterial cell array biosensor. Anal. Biochem. 315(1), 106–113 (2003).
   PubMed Web of Science ®Google Scholar
• Angenendt P, Nyarsik L, Szaflarski W et al. Cell-free protein expression and functional assay in nanowell chip format. Anal. Chem. 76(7), 1844–1849 (2004).
   PubMed Web of Science ®Google Scholar
• Angenendt P, Glökler J, Konthur Z, Lehrach H, Cahill DJ. 3D protein microarrays: performing multiplex immunoassays on a single chip. Anal. Chem. 75(17), 4368–4372 (2003).
   PubMed Web of Science ®Google Scholar
• Angenendt P, Lehrach H, Kreutzberger J, Glökler J. Subnanoliter enzymatic assays on microarrays. Proteomics 5(2), 420–425 (2005).
   PubMed Web of Science ®Google Scholar
• Angenendt P, Wilde J, Kijanka G et al. Seeing better through a MIST: evaluation of monoclonal recombinant antibody fragments on microarrays. Anal. Chem. 76(10), 2916–2921 (2004).
   PubMed Web of Science ®Google Scholar
• Walter G, Konthur Z, Lehrach H. High-throughput screening of surface displayed gene products. Comb. Chem. High Throughput Screen. 4(2), 193–205 (2001).
   PubMed Web of Science ®Google Scholar
• Gao C, Mao S, Lo CH, Wirsching P, Lerner RA, Janda KD. Making artificial antibodies: a format for phage display of combinatorial heterodimeric arrays. Proc. Natl Acad. Sci. USA 96(11), 6025–6030 (1999).
   PubMed Web of Science ®Google Scholar
• Joos TO, Stoll D, Templin MF. Miniaturised multiplexed immunoassays. Curr. Opin. Chem. Biol. 6(1), 76–80 (2002).
   PubMed Web of Science ®Google Scholar
• Rao RS, Visuri SR, McBride MT, Albala JS, Matthews DL, Coleman MA. Comparison of multiplexed techniques for detection of bacterial and viral proteins. J. Proteome Res. 3(4), 736–742 (2004).
   PubMed Web of Science ®Google Scholar
• Lueking A, Possling A, Huber O et al. A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteomics. 2(12), 1342–1349 (2003).
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1(11), 845–867 (2002).
   PubMed Web of Science ®Google Scholar
• Michalet X, Pinaud FF, Bentolila LA et al. Quantum dots for live cells, in vivo imaging, and diagnostics. Science 307(5709), 538–544 (2005).
   PubMed Web of Science ®Google Scholar