Protein and peptide arrays: recent trends and new directions.

Microarrays of proteins and peptides make it possible the screening of thousands of binding events in a parallel and high throughput fashion; therefore they are emerging as a powerful tool for proteomics and clinical assays. The complex nature of Proteome, the wide dynamic range of protein concentration in real samples and the critical role of immobilized protein orientation must be taken into account to maximize the utility of protein microarrays. Immobilization strategy and designing of an ideal local chemical environment on the solid surface are both essential for the success of a protein microarray experiment. This review article will focus on protein and peptide arrays highlighting their technical challenges and presenting new directions by means of a set of selected recent applications.

[1]  E. Kopf,et al.  Panorama™ Ab Microarray Cell Signaling kit: A unique tool for protein expression analysis , 2005, Proteomics.

[2]  R. Frank,et al.  Epitope-targeted proteome analysis: towards a large-scale automated protein–protein-interaction mapping utilizing synthetic peptide arrays , 2003, Analytical and bioanalytical chemistry.

[3]  A. Puisieux,et al.  Protein chip array profiling analysis of sera from neuroblastoma patients. , 2005, Cancer letters.

[4]  Yi-You Huang,et al.  RCA combined nanoparticle-based optical detection technique for protein microarray: a novel approach. , 2004, Biosensors & bioelectronics.

[5]  P. Predki.  Functional protein microarrays: ripe for discovery. , 2004, Current opinion in chemical biology.

[6]  N. Socci,et al.  Profiling bladder cancer using targeted antibody arrays. , 2006, The American journal of pathology.

[7]  M. Snyder,et al.  Analyzing antibody specificity with whole proteome microarrays , 2003, Nature Biotechnology.

[8]  Dieter Stoll,et al.  Protein microarrays: Promising tools for proteomic research , 2003, Proteomics.

[9]  M. Lesaicherre,et al.  Site-specific peptide immobilization strategies for the rapid detection of kinase activity on microarrays. , 2004, Methods in molecular biology.

[10]  P. Predki,et al.  Functional protein microarrays: just how functional are they? , 2005, Current opinion in biotechnology.

[11]  J. Yguerabide,et al.  Light-scattering submicroscopic particles as highly fluorescent analogs and their use as tracer labels in clinical and biological applications. , 1998, Analytical biochemistry.

[12]  S. Wölfl,et al.  Preparation of DNA and protein micro arrays on glass slides coated with an agarose film. , 2000, Nucleic acids research.

[13]  K. Lam,et al.  Peptide and small molecule microarray for high throughput cell adhesion and functional assays. , 2001, Bioconjugate chemistry.

[14]  Emanuel F Petricoin,et al.  Protein microarrays: meeting analytical challenges for clinical applications. , 2003, Cancer cell.

[15]  M. Lesaicherre,et al.  Enzymatic profiling system in a small-molecule microarray. , 2003, Organic letters.

[16]  G. Marko‐Varga,et al.  Integrated protein microchip assay with dual fluorescent- and MALDI read-out. , 2004, Journal of proteome research.

[17]  Andreas D. Baxevanis,et al.  The Molecular Biology Database Collection: an online compilation of relevant database resources , 2000, Nucleic Acids Res..

[18]  Jürgen Kreutzberger,et al.  Bacterial protein microarrays for identification of new potential diagnostic markers for Neisseria meningitidis infections , 2005, Proteomics.

[19]  T. Myers,et al.  Active mixing during hybridization improves the accuracy and reproducibility of microarray results. , 2005, BioTechniques.

[20]  R. Fischer,et al.  Peptide microarrays for the detection of molecular interactions in cellular signal transduction , 2005, Proteomics.

[21]  Yuji Murakami,et al.  Multianalyte immunoassay with self-assembled addressable microparticle array on a chip. , 2003, Analytical biochemistry.

[22]  Lucas J van Vliet,et al.  Nanoarrays: a method for performing enzymatic assays. , 2004, Analytical chemistry.

[23]  Emanuel F Petricoin,et al.  Protein microarray detection strategies: focus on direct detection technologies. , 2004, Journal of immunological methods.

[24]  Gengfeng Zheng,et al.  Multiplexed electrical detection of cancer markers with nanowire sensor arrays , 2005, Nature Biotechnology.

[25]  Kenji Usui,et al.  Protein‐Detecting Microarrays: Current Accomplishments and Requirements , 2005, Chembiochem : a European journal of chemical biology.

[26]  E. Petricoin,et al.  Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front , 2001, Oncogene.

[27]  Jennifer L. Harris,et al.  PNA-encoded protease substrate microarrays. , 2004, Chemistry & biology.

[28]  Dieter Stoll,et al.  Protein microarrays for antibody profiling: Specificity and affinity determination on a chip , 2005, Proteomics.

[29]  C. Niemeyer,et al.  Dendrimer‐Activated Solid Supports for Nucleic Acid and Protein Microarrays , 2001, Chembiochem : a European journal of chemical biology.

[30]  R. Bischoff,et al.  Methodological advances in the discovery of protein and peptide disease markers. , 2004, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[31]  L. Blum,et al.  Design of luminescent biochips based on enzyme, antibody, or DNA composite layers , 2003, Analytical and bioanalytical chemistry.

[32]  M. Lesaicherre,et al.  Antibody-based fluorescence detection of kinase activity on a peptide array. , 2002, Bioorganic & medicinal chemistry letters.

[33]  Bonnie Bruce,et al.  Antigen microarray profiling of autoantibodies in rheumatoid arthritis. , 2005, Arthritis and rheumatism.

[34]  S. Schreiber,et al.  Printing proteins as microarrays for high-throughput function determination. , 2000, Science.

[35]  W. Robinson,et al.  Protein and peptide array analysis of autoimmune disease. , 2002, BioTechniques.

[36]  Ziding Feng,et al.  Optimized Normalization for Antibody Microarrays and Application to Serum-Protein Profiling*S , 2005, Molecular & Cellular Proteomics.

[37]  Y. Berdichevsky,et al.  Versatile protein microarray based on carbohydrate‐binding modules , 2005, Proteomics.

[38]  H. Ge,et al.  UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions. , 2000, Nucleic acids research.

[39]  N. Adey,et al.  Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-microm-thick chamber. , 2002, Analytical chemistry.

[40]  J. She,et al.  Protein microarrays to detect protein-protein interactions using red and green fluorescent proteins. , 2002, Analytical biochemistry.

[41]  P. Lohse,et al.  Generating addressable protein microarrays with PROfusion™ covalent mRNA‐protein fusion technology , 2002, Proteomics.

[42]  J. Hoheisel,et al.  Solid supports for microarray immunoassays , 2003, Journal of molecular recognition : JMR.

[43]  Salvador M. Fernandez,et al.  Grating‐coupled surface plasmon resonance: A cell and protein microarray platform , 2005, Proteomics.

[44]  S. Kingsmore,et al.  Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Gregory L Baker,et al.  Use of porous membranes modified with polyelectrolyte multilayers as substrates for protein arrays with low nonspecific adsorption. , 2006, Analytical chemistry.

[46]  Rémi Desmet,et al.  Peptide-protein microarrays for the simultaneous detection of pathogen infections. , 2004, Bioconjugate chemistry.

[47]  Milan Mrksich,et al.  Peptide arrays: towards routine implementation. , 2004, Current opinion in chemical biology.

[48]  Xiao-Yang Zhu,et al.  Enzymatic activity on a chip: The critical role of protein orientation , 2005, Proteomics.

[49]  L. Liotta,et al.  Proteomic profiling of the cancer microenvironment by antibody arrays , 2001, Proteomics.

[50]  A. Mirzabekov,et al.  Protein microchips: use for immunoassay and enzymatic reactions. , 2000, Analytical biochemistry.

[51]  P. Angenendt.  Progress in protein and antibody microarray technology. , 2005, Drug discovery today.

[52]  H. Koga,et al.  A novel approach to protein expression profiling using antibody microarrays combined with surface plasmon resonance technology , 2005, Proteomics.

[53]  Jonathan M Blackburn,et al.  Fabrication of protein function microarrays for systems-oriented proteomic analysis. , 2005, Methods in molecular biology.

[54]  S. Loefas,et al.  Immobilization of proteins to a carboxymethyldextran-modified gold surface for biospecific interaction analysis in surface plasmon resonance sensors. , 1991, Analytical biochemistry.

[55]  Prem Gurnani,et al.  Pegylated, steptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays. , 2005, Bioconjugate chemistry.

[56]  J. Butler.  Solid supports in enzyme-linked immunosorbent assay and other solid-phase immunoassays. , 2000, Methods.

[57]  H. Sampson,et al.  IgE and IgG4 epitope mapping by microarray immunoassay reveals the diversity of immune response to the peanut allergen, Ara h 2. , 2005, The Journal of allergy and clinical immunology.

[58]  H. Lehrach,et al.  A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. , 1998, Nucleic acids research.

[59]  P. Brown,et al.  Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions , 2001, Genome Biology.

[60]  Joakim Lundeberg,et al.  Serum Microarrays for Large Scale Screening of Protein Levels *S , 2005, Molecular & Cellular Proteomics.

[61]  Patterning protein molecules on poly(ethylene glycol) coated Si(111). , 2004, Biomaterials.

[62]  Srivatsa Venkatasubbarao,et al.  Microarrays--status and prospects. , 2004, Trends in biotechnology.

[63]  Tae Song Kim,et al.  Immunoassay of prostate-specific antigen (PSA) using resonant frequency shift of piezoelectric nanomechanical microcantilever. , 2005, Biosensors & bioelectronics.

[64]  Wayne Thomas,et al.  Microarrayed allergen molecules: diagnostic gatekeepers for allergy treatment , 2002, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[65]  C. Choi,et al.  Current status of protein chip development in terms of fabrication and application , 2003, Proteomics.

[66]  C. Mirkin,et al.  Protein Nanoarrays Generated By Dip-Pen Nanolithography , 2002, Science.

[67]  Marina Cretich,et al.  A new polymeric coating for protein microarrays. , 2004, Analytical biochemistry.

[68]  R. Frank.  The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports--principles and applications. , 2002, Journal of immunological methods.

[69]  Andrea Crisanti,et al.  Antigen microarrays for serodiagnosis of infectious diseases. , 2002, Clinical chemistry.

[70]  S. Kingsmore,et al.  Multiplexed protein profiling on antibody-based microarrays by rolling circle amplification. , 2003, Current opinion in biotechnology.

[71]  Kevin Braeckmans,et al.  Encoding microcarriers: present and future technologies , 2002, Nature Reviews Drug Discovery.

[72]  R. Wiese.  Analysis of several fluorescent detector molecules for protein microarray use. , 2003, Luminescence : the journal of biological and chemical luminescence.

[73]  Marcella Chiari,et al.  Characterization of a polymeric adsorbed coating for DNA microarray glass slides. , 2004, Analytical chemistry.

[74]  Wolfgang Huber,et al.  Systematic comparison of surface coatings for protein microarrays , 2005, Proteomics.

[75]  Eun Jeong Cho,et al.  Production and processing of aptamer microarrays. , 2005, Methods.

[76]  M. W. Mueller,et al.  Allergen microarray: comparison of microarray using recombinant allergens with conventional diagnostic methods to detect allergen‐specific serum immunoglobulin E , 2003, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[77]  E. Petricoin,et al.  Reverse-phase protein microarrays for tissue-based analysis. , 2005, Current opinion in molecular therapeutics.

[78]  J. Katzenellenbogen,et al.  A Proteomic Microarray Approach for Exploring Ligand-initiated Nuclear Hormone Receptor Pharmacology, Receptor Selectivity, and Heterodimer Functionality* , 2005, Molecular & Cellular Proteomics.

[79]  Petra Pavlickova,et al.  Application of self‐assembly techniques in the design of biocompatible protein microarray surfaces , 2002, Electrophoresis.

[80]  Dongku Kang,et al.  High-Throughput Screening of Novel Peptide Inhibitors of an Integrin Receptor from the Hexapeptide Library by Using a Protein Microarray Chip , 2004, Journal of biomolecular screening.

[81]  G. Gordon,et al.  Hybridization enhancement using microfluidic planetary centrifugal mixing. , 2004, Analytical chemistry.

[82]  M. Mrksich,et al.  Peptide chips for the quantitative evaluation of protein kinase activity , 2002, Nature Biotechnology.

[83]  Bhupinder Bhullar,et al.  Self-Assembling Protein Microarrays , 2004, Science.

[84]  M. Coleman,et al.  High-throughput, fluorescence-based screening for soluble protein expression. , 2004, Journal of proteome research.

[85]  Kit S. Lam,et al.  Protein and Chemical Microarrays—Powerful Tools for Proteomics , 2003, Journal of biomedicine & biotechnology.

[86]  M. Gerstein,et al.  Analysis of yeast protein kinases using protein chips , 2000, Nature Genetics.

[87]  P. Brown,et al.  Autoantigen microarrays for multiplex characterization of autoantibody responses , 2002, Nature Medicine.

[88]  Barry Schweitzer,et al.  Microarrays to characterize protein interactions on a whole‐proteome scale , 2003, Proteomics.

[89]  Y. Okahata,et al.  Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance. , 2001, Biochemistry.

[90]  C. Borrebaeck,et al.  High-throughput proteomics using antibody microarrays , 2004, Expert review of proteomics.

[91]  S. Nock,et al.  Generation of bioreagents for protein chips , 2003, Proteomics.

[92]  Yong Li,et al.  Protein recognition via surface molecularly imprinted polymer nanowires. , 2006, Analytical chemistry.

[93]  R. Longhi,et al.  Peptide microarrays for the characterization of antigenic regions of human chromogranin A , 2005, Proteomics.

[94]  M. Snyder,et al.  Protein chip technology. , 2003, Current opinion in chemical biology.

[95]  Jizhong Zhou,et al.  Protein microarrays on hybrid polymeric thin films prepared by self‐assembly of polyelectrolytes for multiple‐protein immunoassays , 2006, Proteomics.

[96]  Joshua LaBaer,et al.  Emerging tools for real‐time label‐free detection of interactions on functional protein microarrays , 2005, The FEBS journal.

[97]  Wanzhi Huang,et al.  A broad-spectrum peptide inhibitor of beta-lactamase identified using phage display and peptide arrays. , 2003, Protein engineering.

[98]  Yoonsuk Lee,et al.  ProteoChip: A highly sensitive protein microarray prepared by a novel method of protein immobilization for application of protein‐protein interaction studies , 2003, Proteomics.