ProtoArray® microarrays are high-density, functional protein microarrays that enable rapid elucidation of protein interactions on a proteome scale. For your convenience, we have complied references that describe applications of this powerful technology.

Pathogen Detection

  • Fernandez S et al. (2011) Antibody Recognition of the Dengue Virus Proteome and Implications for Development of Vaccines. Clin. Vaccine Immunol. 18: 523-532.
  • Keasey SL et al. (2009) Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis. Mol Cell Proteomics. 8: 924-935.

Immune Response Biomarker Profiling

  • Sidgel et al. (2012) Non-HLA Antibodies to Immunogenic Epitopes Predict the Evolution of Chronic Renal Allograft Injury. J Am Soc Nephrol. 23: 750-763.
  • Chen R et al. (2012) Personalized Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes. Cell 148: 1293-1307.
  • Liu M et al. (2012) Immune responses to self-antigens in asthma patients: clinical and immunopathological implications. Hum Immunol. 73: 511-516.
  • Postow MA et al. (2012) Immunologic correlates of the abscopal effect in a patient with melanoma. NEJM. 366: 925-931.
  • Han M et al. (2012) Diagnosis of Parkinson’s disease based on disease-specific autoantibody profiles in human sera. PLoS One. 7: e32383.
  • Mangé A et al. (2012) Serum autoantibody signature of ductal carcinoma in situ progression to invasive breast cancer. Clin Cancer Res. 18: 1992-2000.
  • Wood JD et al. (2012) Anti-Enteric Neuronal Antibodies and the Irritable Bowel Syndrome. J Neurogastroenterol Motil. 18: 78-85.
  • Biernacki MA et al. (2012) Novel myeloma-associated antigens revealed in the context of syngeneic
  • hematopoietic stem cell transplantation. Blood. 119: 3142-3150.
  • Sigdel TK et al. (2011) Profiling of Autoantibodies in IgA Nephropathy, an Integrative Antibiomics Approach. Clin J Am Soc Nephrol. 6: 2775-2784.
  • Jansen FH et al. (2011) Profiling of antibody production against xenograft-released proteins by protein microarrays discovers prostate cancer markers. J. Proteome Res. 11: 728-735.
  • Winer DA et al. (2011) B cells promote insulin resistance through modulation of T cells and production of pathogenic IgG antibodies. Nat. Med 17: 610-618.
  • Hu S et al. (2011) Identification of autoantibody biomarkers for primary Sjögren’s syndrome using protein microarrays. Proteomics. 11: 1499-1507.
  • Nagele E et al. (2011) Diagnosis of Alzheimer's disease based on disease-specific autoantibody profiles in human sera. PLoS One. 6: e23112.
  • Dinavahi R et al. (2011) Antibodies reactive to non-HLA antigens in transplant glomerulopathy. J Am Soc Nephrol. 22: 1168-1178.
  • Vermeulen N et al. (2011) Identification of a novel autoantigen in inflammatory bowel disease by a protein microarray. Inflamm Bowel Dis. 17: 1291-1300.
  • Butte AJ et al. (2011) Protein Microarrays Discover Angiotensinogen and PRKRIP1 as Novel Targets for Autoantibodies in Chronic Renal Disease. Mol Cell Proteomics. 10: M110.000497.
  • Gnjatic S et al. (2010) Seromic profiling of ovarian and pancreatic cancer. Proc. Natl. Acad. Sci. USA, 107: 5088–5093.
  • Le Roux S et al. (2010) Biomarkers for the Diagnosis of the Stable Kidney Transplant and Chronic Transplant Injury Using the ProtoArray® Technology. Transplant Proc. 42: 3475-3481
  • Nguyen MC et al. (2010) Antibody responses to galectin-8, TARP and TRAP1 in prostate cancer patients treated with a GM-CSF-secreting cellular immunotherapy. Cancer Immunol Immunother. 59:1313-1323.
  • Porcheray F et al. (2010) Chronic Humoral Rejection of Human Kidney Allografts Associates With Broad Autoantibody Responses. Transplantation. 89: 1239-1246.
  • Jarius S et al. (2010) A new Purkinje cell antibody (anti-Ca) associated with subacute cerebellar ataxia: immunological characterization. J Neuroinflammation. 7: 21.
  • Orenes-Piñero E et al. (2010) Serum and Tissue Profiling in Bladder Cancer Combining Protein and Tissue Arrays. J Proteome Res. 9: 164-173.
  • Marina O et al. (2010) Serologic Markers of Effective Tumor Immunity against Chronic Lymphocytic Leukemia Include Nonmutated B-Cell Antigens. Cancer Res. 70: 1344-1355.
  • Li L et al. (2010) Compartmental Localization and Clinical Relevance of MICA Antibodies After Renal Transplantation. Transplantation. 89: 312-319.
  • Wadia PP et al. (2010) Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. Blood. 115: 2077-2087.
  • Biernacki MA et al. (2010) Efficacious immune therapy in chronic myelogenous leukemia (CML) recognizes antigens that are expressed on CML progenitor cells. Cancer Res. 70: 906–915.
  • Schweitzer B et al. (2010) Immune response biomarker profiling application on ProtoArray protein microarrays. Methods Mol Biol. 641:243-52.
  • Babel I et al. (2009) Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays. Mol Cell Proteomics. 8: 2382–2395.
  • Sutherland SM et al. (2009) Protein microarrays identify antibodies to protein kinase Cζ that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Kidney Int. 76: 1277–1283.
  • Li L et al. (2009) Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures. Proc Natl Acad Sci USA. 106: 4148–4153.
  • Auger I et al. (2009) New autoantigens in rheumatoid arthritis: screening 8268 protein arrays with RA patients’ sera. Ann Rheum Dis. 68: 591–594.
  • Gunawardana CG et al. (2009) Identifying novel autoantibody signatures in ovarian cancer using high-density protein microarrays. Clin Biochem. 42: 426–429.
  • Gnjatic S et al. (2009) Seromic analysis of antibody responses in non-small cell lung cancer patients and healthy donors using conformational protein arrays. J Immunol Methods. 341: 50–58.
  • Roche S et al. (2008) Autoantibody profiling on high-density protein microarrays for biomarker discovery in the cerebrospinal fluid. J Immunol Methods. 338: 75-78.
  • Hudson ME et al. (2007) Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci USA. 104: 17494-17499.
  • Lubomirski M et al. (2007) A consolidated approach to analyzing data from high-throughput protein microarrays with an application to immune response profiling in humans. J Comput Biol. 14: 350-359.
  • Lalive PH et al. (2006) Identification of new serum autoantibodies in neuromyelitis optica using protein microarrays. Neurology. 67: 176-177.
  • Mattoon D et al. (2005) Biomarker discovery using protein microarray technology platforms: Antibody-antigen complex profiling. Expert Rev Proteomics. 2: 879-889.

Protein-Protein Interactions

  • Meehan M et al. (2012) Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase oncogene. Mol Cancer. 11: 6.
  • Storm P et al. (2011) Conserved features of cancer cells define their sensitivity to HAMLET-induced death; c-Myc and glycolysis. Oncogene. 30: 4765–4779.
  • De Denato M et al. (2011) Class III β-tubulin and the cytoskeletal gateway for drug resistance in ovarian cancer. J Cell Physiol. 227: 1034-1041.
  • Babij C et al. (2011) STK33 kinase activity is nonessential in KRAS-dependent cancer cells. Cancer Res. 71: 5818-5826.
  • Lee HK et al. (2011) Odontogenic ameloblasts-associated protein (ODAM), via phosphorylation by bone morphogenetic protein receptor type IB (BMPR–IB), is implicated in ameloblast differentiation. J Cell Biochem. 113: 1754-1765.
  • Virok DP et al. (2011) Protein Array Based Interactome Analysis of Amyloid-β Indicates an Inhibition of Protein Translation. J. Proteome Res. 10: 1538–1547.
  • Wu YY et al. (2011) SCUBE3 is an endogenous TGF-b receptor ligand and regulates the epithelial-mesenchymal transition in lung cancer. Oncogene 30: 3682–3693.
  • Analysis Of LNX1 Interacting Proteins. PLoS One 6: e26248.
  • Echtenkamp FJ et al. (2011) Global Functional Map of the p23 Molecular Chaperone Reveals an Extensive Cellular Network. Molecular Cell 43: 229–241. 10. Bauer M et al. (2011) Protein networks involved in vesicle fusion, transport, and storage revealed by array-based proteomics. Methods Mol Biol. 781: 47-58.
  • Olah J et al. (2011) Interactions of Pathological Hallmark Proteins: Tubulin Polymerization Promoting protein/p25, β-Amyloid, and α-Synuclein. J Biol Chem. 286: 34088-34100.
  • Li D et al (2011) Binding of Lactoferrin to IGBP1 Triggers Apoptosis in a Lung Adenocarcinoma Cell Line. Anticancer Res. 31: 529-534.
  • Al-Mulla F et al (2011) Raf Kinase Inhibitor Protein RKIP Enhances Signaling by Glycogen Synthase Kinase-3 β. Cancer Res. 71: 1334-1343.
  • Morikawa H et al. (2010) The bacterial effector Cif interferes with SCF ubiquitin ligase function by inhibiting deneddylation of Cullin1. Biochem Biophys Res Commun. 401: 268-274.
  • Paidas MJ et al. (2010) A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells. Am J Obstet Gynecol. 202:459.e1-8.
  • Sumiyoshi K et al. (2010) Protein microarray analysis identifies cyclic nucleotide phosphodiesterase as an interactor of Nogo-A. Neuropathology. 30: 7–14.
  • Fenner BJ et al. (2010) Expanding the Substantial Interactome of NEMO Using Protein Microarrays. PLoS One. 5: e8799.
  • Tong Y et al. (2008) Pituitary tumor transforming gene 1 regulates Aurora kinase A activity. Oncogene. 27: 6385–6395.
  • Schnack C et al. (2008) Protein array analysis of oligomerizatin-induced changes in alpha-synuclein protein-protein interactions points to an interference with Cdc42 effector proteins. Neuroscience. 154: 1450–1457.
  • Li Z. et al. (2008). Cdc34p ubiquitin-conjugating enzyme is a component of the tombusvirus replicase complex and ubiquitinates p33 replication protein. J Virol. 82: 6911-6926.
  • Satoh J et al. (2008). Protein microarray analysis identifies human cellular prion protein interactors. Neuropathol Appl Neurobiol. 35: 16–35.
  • Poltermann S et al. (2007) Gpm1p is a Factor H-, FHL-1-, and plasminogen-binding surface protein of Candida albicans. J Biol Chem. 282: 37537-37544.
  • Salamat-Miller N et al. (2007) A network-based analysis of polyanion-binding proteins utilizing human protein arrays. J Biol Chem. 282: 10153-10163.
  • Satoh J et al. (2006) Rapid identification of 14-3-3-binding proteins by protein microarray analysis. J Neurosci Methods. 152: 278-288.
  • Salamat-Miller N et al. (2006) A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays. Mol Cell Proteomics. 5: 2263-2278.
  • Jin F. et al. (2006) A pooling-deconvolution strategy for biological network elucidation. Nat Methods. 3: 183-189.
  • Hesselberth J et al. (2006) Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol. 7: R30.

Kinsase Substrate Interactions

  • Kinuka I et al. (2012) cGMP-dependent protein kinase I promotes cell apoptosis through hyperactivation of death-associated protein kinase 2. Biochem and Biophys Res Commun. 422: 2.
  • Kottom TJ and Limper AH. (2011) Substrate analysis of the Pneumocystis carinii protein kinases PcCbk1 and PcSte20 using yeast proteome microarrays provides a novel method for Pneumocystis signalling biology. Yeast. 10: 707-719.
  • De la Mota-Peynado A et al. (2011) Identification of the atypical MAPK Erk3 as a novel substrate for p21-activated kinase (Pak) activity. J Biol Chem. 286: 13603-13611.
  • Schnack C et al. (2008). Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high-density protein microarrays. Proteomics. 8: 1980-1986.
  • Meng L et al. (2008) Protein kinase substrate identification on functional protein arrays. BMC Biotechnol. 8: 22.
  • Boyle SN et al. (2007) A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsalwave formation. Curr Biol. 17: 1-7.
  • Ptacek J et al. (2005) Global analysis of protein phosphorylation in yeast. Nature. 438: 679-684.
  • Mah A et al. (2005) Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening. BMC Biochem. 6: 22.

Antibody Specificity Profiling

  • Stafford P et al. (2012) Physical Characterization of the “Immunosignaturing Effect”. Mol Cell Proteomics 11: M111.011593.
  • Diehnelt CW et al. (2010) Discovery of High-Affinity Protein Binding Ligands – Backwards. PLoS One. 5: e10728.
  • Predki PF et al. (2005) Protein microarrays: A new tool for profiling antibody cross-reactivity. Hum Antibodies. 14: 7-15.
  • Bangham R et al. (2005) Protein microarray-based screening of antibody specificity. Methods Mol Med. 114: 173-182.
  • Michaud GA et al. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol. 21: 1509-1512.

Small Molecule Interactions

  • To C et al. (2010) Synthetic Triterpenoids Target the ARP2/3 Complex and Inhibit Branched Actin Polymerization. JBC. 285: 27944-27957.
  • Conrad A et al. (2010) Proteomic Analysis of Potential Keratan Sulfate, Chondroitin Sulfate A, and Hyaluronic Acid Molecular Interactions. Invest Ophthalmol Vis Sci. 51: 4500-4515.
  • Singh J et al. (2008) DcpS as a therapeutic target for spinal muscular atrophy. ACS Chem Biol. 3: 711–722.

Post Translation Modification Profiling

  • Levy D et al. (2011) A proteomic approach for the identification of novel lysine methyltransferase substrates. Epigenetics & Chromatin. 4: 19.
  • Loch CM et al. (2011) Protein Microarrays for the Identification of Praja1 E3 Ubiquitin Ligase Substrates Cell Biochem Biophys. 60: 127–135.
  • Troiani S et al. (2011) Identification of candidate substrates for Poly(ADP-ribose) polymerase-2 (PARP2) in the absence of DNA damage using high-density protein microarrays. FEBS J. 278: 3676-3687.
  • Rincón et al. (2010) Development and Validation of a Method for Profiling Post-Translational Modification Activities Using Protein Microarrays. PLoS One. 5: e11332.
  • Merbl Y and Kirschner MW. (2009) Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. Proc Natl Acad Sci USA. 106: 2543-8.
  • Tao et al. (2009) Studies of the Expression of Human Poly(ADP-ribose) Polymerase-1 in Saccharomyces cerevisiae and Identification of PARP-1 Substrates by Yeast Proteome Microarray Screening. Biochemistry 48: 11745–11754.
  • Lin Y et al. (2009) Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136: 1073–1084.
  • Gupta R. et al. (2007) Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Systems Biol. 3: 1-12.

DNA/RNA-Protein Interactions

  • Scherrer T et al (2010) A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PLoS One. 5: e15499.
  • Hu S et al. (2009) Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling. Cell. 139: 610-622.
  • Hall D. et al. (2004) Regulation of gene expression by a metabolic enzyme. Science. 306: 482-484.

Reviews

  • Luo M. (2012) Current Chemical Biology Approaches to Interrogate Protein Methyltransferases. ACS Chem Biol. 7: 443-463.
  • DesMetz C et al. (2011) Autoantibody signatures: progress and perspectives for early cancer detection.J Cell Mol Med. 15: 2013–2024.
  • Yang L et al. (2011) Protein microarrays for systems biology. Acta Biochim Biophys. Sin 43: 161–171.
  • Martin K et al (2011) Exploring the Immunoproteome for Ovarian Cancer Biomarker Discovery Int. J. Mol. Sci. 12: 410-428.
  • Vaughan R and Sacks S. (2010) Genomics in human renal transplantation. Curr Opin Immunol. 22: 689-93.
  • Wu T et al. (2010) Biomarkers of rheumatoid arthritis: recent progress. Exp Op Med Diag. 4: 293-305.
  • Naesens M and Sarwal MM. (2010) Molecular Diagnostics in Transplantation. Nat Rev Nephrol. 6: 614-628.
  • Michaud GA et al. (2006) Functional protein arrays to facilitate drug discovery and development. IDrugs. 9: 266-272.
  • Michaud GA et al. (2006) Applications of protein arrays for small molecule drug discovery and characterization. Biotechnol Genet Eng Rev. 22: 197-211.
  • Merkel J et al. (2005) Functional protein microarrays: Just how functional are they? Curr Opin Biotechnol Rev. 16: 447-452.
  • Zhou FX et al. (2004) Development of functional protein microarrays for drug discovery: Progress and challenges. Comb Chem High Throughput Screen. 7: 539-546.
  • Predki PF (2004) Functional protein microarrays: Ripe for discovery. Curr Opin Chem Biol. 8: 8-13.
  • Schweitzer B et al. (2003) Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics. 3: 2190-2199.
  • Michaud GA and Snyder M (2002) Proteomic approaches for the global analysis of proteins. Biotechniques. 33: 1308-1316.
  • Zhu H et al. (2001) Global analysis of protein activities using proteome chips. Science. 293: 2101-2105.

Book Chapters

  • DeLuca DS, Marina O, Ray S, Zhang GL, Wu CJ, and Brusic V (2011) Data Processing and Analysis for Protein Microarrays. In Catherine J. Wu (ed.), Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, vol. 723 (pp 337-347) Springer Science+Business Media.
  • Smith MG, Ptacek J, & Snyder M (2011) Kinase Substrate Interactions. In Catherine J. Wu (ed.), Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, vol. 723 (pp 201-212) Springer Science+Business Media.
  • Wadia PP, Sahaf B, & Miklos DB (2011) Recombinant Antigen Microarrays for Serum/Plasma Antibody Detection. In Catherine J. Wu (ed.), Protein Microarray for Disease Analysis: Methods and Protocols, Methods in Molecular Biology, vol. 723 (pp 81-104) Springer Science+Business Media.
  • Persaud A & Rotin D (2011) Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases. In Castrillo JI & Oliver SG (eds.), Yeast Systems Biology, Methods in Molecular Biology, vol 759 (pp 215-224) Springer Science+Business Media.