Systematic antibody and antigen-based proteomic profiling with microarrays

References

• Hanash S. Disease proteomics. Nature422, 226–232 (2003).
   PubMed Web of Science ®Google Scholar
• Hu S, Loo JA, Wong DT. Human body fluid proteome analysis. Proteomics6(23), 6326–6353 (2006).
   PubMed Web of Science ®Google Scholar
• Ahn S-M, Simpson RJ. Body fluid proteomics: prospects for biomarker discovery. Proteomics Clin. Appl.1(9), 1004–1015 (2007).
   PubMed Web of Science ®Google Scholar
• von Neuhoff N, Pich A. Mass spectrometry-based methods for biomarker detection and analysis. Drug Discov. Today Technol.2(4), 361–367 (2005).
   PubMedGoogle Scholar
• Domon B, Aebersold R. Mass spectrometry and protein analysis. Science312(5771), 212–217 (2006).
   PubMed Web of Science ®Google Scholar
• Cravatt BF, Simon GM, Yates JR 3rd. The biological impact of mass-spectrometry-based proteomics. Nature450(7172), 991–1000 (2007).
   PubMed Web of Science ®Google Scholar
• Canas B, Lopez-Ferrer D, Ramos-Fernandez A, Camafeita E, Calvo E. Mass spectrometry technologies for proteomics. Brief Funct. Genomic. Proteomic.4(4), 295–320 (2006).
   PubMedGoogle Scholar
• Zhao Y, Lee W-NP, Xiao GG. Quantitative proteomics and biomarker discovery in human cancer. Expert Rev. Proteomics6(2), 115–118 (2009).
   PubMed Web of Science ®Google Scholar
• Silberring J, Ciborowski P. Biomarker discovery and clinical proteomics. Trends Analyt. Chem.29(2), 128–128 (2010).
   PubMed Web of Science ®Google Scholar
• Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol.3(1), 33–44 (2009).
   PubMed Web of Science ®Google Scholar
• Kulasingam V, Diamandis EP. Strategies for discovering novel cancer biomarkers through utilization of emerging technologies. Nat. Clin. Pract. Oncol.5(10), 588–599 (2008).
   PubMedGoogle Scholar
• Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotech.24(8), 971–983 (2006).
   PubMed Web of Science ®Google Scholar
• Hellström M, Jonmarker S, Lehtiö J, Auer G, Egevad L. Proteomics in clinical prostate research. Proteomics Clin. Appl.1(9), 1058–1065 (2007).
   PubMed Web of Science ®Google Scholar
• Steuber T, Helo P, Lilja H. Circulating biomarkers for prostate cancer. World J. Urol.25(2), 111–119 (2007).
   PubMed Web of Science ®Google Scholar
• Birkhahn M, Mitra AP, Cote RJ. Molecular markers for bladder cancer: the road to a multimarker approach. Expert Rev. Anticancer Ther.7(12), 1717–1727 (2007).
   PubMed Web of Science ®Google Scholar
• Ikonomidis I, Michalakeas CA, Lekakis J, Paraskevaidis I, Kremastinos DT. Multimarker approach in cardiovascular risk prediction. Dis. Markers26(5), 273–285 (2009).
   PubMed Web of Science ®Google Scholar
• Ekins RP. Multi-analyte immunoassay. J. Pharm. Biomed. Anal.7(2), 155–168 (1989).
   PubMed Web of Science ®Google Scholar
• MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science289(5485), 1760–1763 (2000).
   PubMed Web of Science ®Google Scholar
• Templin MF, Stoll D, Schwenk JM et al. Protein microarrays: promising tools for proteomic research. Proteomics3(11), 2155–2166 (2003).
   PubMed Web of Science ®Google Scholar
• Fulton RJ, McDade RL, Smith PL, Kienker LJ. Advanced multiplexed analysis with the FlowMetrix. Clin. Chem.1756, 1749–1756 (1997).
   Google Scholar
• Wu W, Slastad H, de la Rosa Carrillo D et al. Antibody array analysis with label-based detection and resolution of protein size. Mol. Cell Proteomics8(2), 245–257 (2009).
   PubMed Web of Science ®Google Scholar
• Templin MF, Stoll D, Bachmann J, Joos TO. Protein microarrays and multiplexed sandwich immunoassays: what beats the beads? Comb. Chem. High Throughput Screen.7(3), 223–229 (2004).
   PubMed Web of Science ®Google Scholar
• Stoevesandt O, Taussig MJ, He M. Protein microarrays: high-throughput tools for proteomics. Expert Rev. Proteomics6(2), 145–157 (2009).
   PubMed Web of Science ®Google Scholar
• Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P. The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin. Appl.2(10–11), 1386–1402 (2008).
   PubMed Web of Science ®Google Scholar
• Polanski M, Anderson NL, Polanski M, Anderson NL. A list of candidate cancer biomarkers for targeted proteomics. Biomark. Insights7(1), 1–48 (2007).
   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
• Poetz O, Schwenk JM, Kramer S et al. Protein microarrays: catching the proteome. Mech. Ageing Dev.126(1), 161–170 (2005).
   PubMed Web of Science ®Google Scholar
• Haab BB. Methods and applications of antibody microarrays in cancer research. Proteomics3(11), 2116–2122 (2003).
   PubMed Web of Science ®Google Scholar
• Yu X, Schneiderhan-Marra N, Joos TO. Protein microarrays for personalized medicine. Clin. Chem.56(3), 376–387 (2010).
   PubMed Web of Science ®Google Scholar
• Falk R, Ramstrom M, Stahl S, Hober S. Approaches for systematic proteome exploration. Biomol. Eng.24(2), 155–168 (2007).
   PubMedGoogle Scholar
• Tomizaki KY, Usui K, Mihara H. Protein-detecting microarrays: current accomplishments and requirements. Chembiochem.6(5), 782–799 (2005).
   PubMed Web of Science ®Google Scholar
• De Jager W, Te Velthuis H, Prakken BJ, Kuis W, Rijkers GT. Simultaneous detection of 15 human cytokines in a single sample of stimulated peripheral blood mononuclear cells. Clin. Diagn. Lab. Immunol.10(1), 133–139 (2003).
   PubMedGoogle Scholar
• Hsu HY, Wittemann S, Joos TO. Miniaturized parallelized sandwich immunoassays. Methods Mol. Biol.428, 247–261 (2008).
   PubMedGoogle Scholar
• Poetz O, Henzler T, Hartmann M et al. Sequential multiplex analyte capturing for phospho-protein profiling. Mol. Cell Proteomics DOI: 10.1074/mcp.M110.002709 (2010) (Epub ahead of print).
   Google Scholar
• Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat. Rev. Drug Discov.5(4), 310–320 (2006).
   PubMed Web of Science ®Google Scholar
• Darmanis S, Nong RY, Hammond M et al. Sensitive plasma protein analysis by microparticle-based proximity ligation assays. Mol. Cell Proteomics9(2), 327–335 (2010).
   PubMed Web of Science ®Google Scholar
• Schallmeiner E, Oksanen E, Ericsson O et al. Sensitive protein detection via triple-binder proximity ligation assays. Nat. Methods4(2), 135–137 (2007).
   PubMed Web of Science ®Google Scholar
• Rissin DM, Kan CW, Campbell TG et al. Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nat. Biotechnol.28(6), 595–599 (2010).
   PubMed Web of Science ®Google Scholar
• Wingren C, Borrebaeck CA. Antibody microarray analysis of directly labelled complex proteomes. Curr. Opin. Biotechnol.19(1), 55–61 (2008).
   PubMed Web of Science ®Google Scholar
• Kusnezow W, Banzon V, Schroder C et al. Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies. Proteomics7(11), 1786–1799 (2007).
   PubMed Web of Science ®Google Scholar
• Schroder C, Jacob A, Tonack S et al. Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies. Mol. Cell Proteomics9(6), 1271–1280 (2010).
   PubMed Web of Science ®Google Scholar
• Schwenk JM, Gry M, Rimini R, Uhlen M, Nilsson P. Antibody suspension bead arrays within serum proteomics. J. Proteome Res.7(8), 3168–3179 (2008).
   PubMed Web of Science ®Google Scholar
• Schwenk JM, Igel U, Neiman M et al. Towards next generation plasma profiling via heat-induced epitope retrieval and array-based assays. Mol. Cell Proteomics (2010).
   PubMed Web of Science ®Google Scholar
• Uhlén M. Affinity as a tool in life science. Biotechniques44(5), 649–654 (2008).
   PubMed Web of Science ®Google Scholar
• Taussig MJ, Stoevesandt O, Borrebaeck CA et al. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat. Methods4(1), 13–17 (2007).
   PubMed Web of Science ®Google Scholar
• Bjorling E, Uhlen M. Antibodypedia, a portal for sharing antibody and antigen validation data. Mol. Cell Proteomics7(10), 2028–2037 (2008).
   PubMed Web of Science ®Google Scholar
• Berglund L, Bjorling E, Oksvold P et al. A genecentric human protein atlas for expression profiles based on antibodies. Mol. Cell Proteomics7(10), 2019–2027 (2008).
   PubMed Web of Science ®Google Scholar
• Schofield DJ, Pope AR, Clementel V et al. Application of phage display to high throughput antibody generation and characterization. Genome Biol.8(11), R254 (2007).
   PubMed Web of Science ®Google Scholar
• Uhlen M, Graslund S, Sundstrom M. A pilot project to generate affinity reagents to human proteins. Nat. Methods5(10), 854–855 (2008).
   PubMed Web of Science ®Google Scholar
• Haab BB, Paulovich AG, Anderson NL et al. A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report. Mol. Cell Proteomics5(10), 1996–2007 (2006).
   PubMed Web of Science ®Google Scholar
• De Masi F, Chiarella P, Wilhelm H et al. High throughput production of mouse monoclonal antibodies using antigen microarrays. Proteomics5(16), 4070–4081 (2005).
   PubMed Web of Science ®Google Scholar
• Rieger M, Cervino C, Sauceda JC, Niessner R, Knopp D. Efficient hybridoma screening technique using capture antibody based microarrays. Anal. Chem.81(6), 2373–2377 (2009).
   PubMed Web of Science ®Google Scholar
• Uhlen M, Björling E, Agaton C et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell Proteomics4(12), 1920–1932 (2005).
   PubMed Web of Science ®Google Scholar
• Pontén F, Jirström K, Uhlén M. The Human Protein Atlas – a tool for pathology. J. Pathol.216(4), 387–393 (2008).
   PubMed Web of Science ®Google Scholar
• Nilsson P, Paavilainen L, Larsson K et al. Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling. Proteomics5(17), 4327–4337 (2005).
   PubMed Web of Science ®Google Scholar
• Schwenk JM, Igel U, Kato BS et al. Comparative protein profiling of serum and plasma using an antibody suspension bead array approach. Proteomics10(3), 532–540 (2010).
   PubMed Web of Science ®Google Scholar
• Rockberg J, Lofblom J, Hjelm B, Uhlen M, Stahl S. Epitope mapping of antibodies using bacterial surface display. Nat. Methods5(12), 1039–1045 (2008).
   PubMed Web of Science ®Google Scholar
• Rockberg J, Schwenk JM, Uhlen M. Discovery of epitopes for targeting the human epidermal growth factor receptor 2 (HER2) with antibodies. Mol Oncol. DOI: 10.1016/j.molonc.2009.01.003 (2009) (Epub ahead of print).
   PubMed Web of Science ®Google Scholar
• Pansri P, Jaruseranee N, Rangnoi K, Kristensen P, Yamabhai M. A compact phage display human scFv library for selection of antibodies to a wide variety of antigens. BMC Biotechnol.9, 6 (2009).
   PubMed Web of Science ®Google Scholar
• Kwong KY, Baskar S, Zhang H, Mackall CL, Rader C. Generation, affinity maturation, and characterization of a human anti-human NKG2D monoclonal antibody with dual antagonistic and agonistic activity. J. Mol. Biol.384(5), 1143–1156 (2008).
   PubMed Web of Science ®Google Scholar
• Schoonbroodt S, Steukers M, Viswanathan M et al. Engineering antibody heavy chain CDR3 to create a phage display Fab library rich in antibodies that bind charged carbohydrates. J. Immunol.181(9), 6213–6221 (2008).
   PubMed Web of Science ®Google Scholar
• Yang HY, Kang KJ, Chung JE, Shim H. Construction of a large synthetic human scFv library with six diversified CDRs and high functional diversity. Mol. Cells27(2), 225–235 (2009).
   PubMed Web of Science ®Google Scholar
• Zhao XL, Chen WQ, Yang ZH et al. Selection and affinity maturation of human antibodies against rabies virus from a scFv gene library using ribosome display. J. Biotechnol.144(4), 253–258 (2009).
   PubMed Web of Science ®Google Scholar
• Kronqvist N, Lofblom J, Jonsson A, Wernerus H, Stahl S. A novel affinity protein selection system based on staphylococcal cell surface display and flow cytometry. Protein Eng. Des. Sel.21(4), 247–255 (2008).
   PubMed Web of Science ®Google Scholar
• Walker LM, Bowley DR, Burton DR. Efficient recovery of high-affinity antibodies from a single-chain Fab yeast display library. J. Mol. Biol.389(2), 365–375 (2009).
   PubMed Web of Science ®Google Scholar
• Nord K, Gunneriusson E, Ringdahl J et al. Binding proteins selected from combinatorial libraries of an α-helical bacterial receptor domain. Nat. Biotechnol.15(8), 772–777 (1997).
   PubMed Web of Science ®Google Scholar
• Lofblom J, Feldwisch J, Tolmachev V et al. Affibody molecules: engineered proteins for therapeutic, diagnostic and biotechnological applications. FEBS Lett.584(12), 2670–2680 (2010).
   PubMed Web of Science ®Google Scholar
• Brody EN, Gold L. Aptamers as therapeutic and diagnostic agents. J. Biotechnol.74(1), 5–13 (2000).
   PubMedGoogle Scholar
• Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science249(4968), 505–510 (1990).
   PubMed Web of Science ®Google Scholar
• Rowe W, Platt M, Day PJ. Advances and perspectives in aptamer arrays. Integr. Biol. (Camb.)1(1), 53–58 (2009).
   PubMed Web of Science ®Google Scholar
• Ostroff R, Foreman T, Keeney TR et al. The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J. Proteomics73(3), 649–666 (2010).
   PubMed Web of Science ®Google Scholar
• Zahnd C, Wyler E, Schwenk JM et al. A designed ankyrin repeat protein evolved to picomolar affinity to HER2. J. Mol. Biol.369(4), 1015–1028 (2007).
   PubMed Web of Science ®Google Scholar
• Bossi A, Bonini F, Turner AP, Piletsky SA. Molecularly imprinted polymers for the recognition of proteins: the state of the art. Biosens. Bioelectron.22(6), 1131–1137 (2007).
   PubMed Web of Science ®Google Scholar
• Katrlik J, Svitel J, Gemeiner P, Kozar T, Tkac J. Glycan and lectin microarrays for glycomics and medicinal applications. Med. Res. Rev.30(2), 394–418 (2010).
   PubMed Web of Science ®Google Scholar
• Uttamchandani M, Walsh DP, Yao SQ, Chang YT. Small molecule microarrays: recent advances and applications. Curr. Opin. Chem. Biol.9(1), 4–13 (2005).
   PubMed Web of Science ®Google Scholar
• Tegel H, Steen J, Konrad A et al. High-throughput protein production – lessons from scaling up from 10 to 288 recombinant proteins per week. Biotechnology J.4(1), 51–57 (2009).
   PubMedGoogle Scholar
• Gräslund S, Nordlund P, Weigelt J, Hallberg BM. Protein production and purification. Nat. Methods5(2), 135–146 (2008).
   PubMed Web of Science ®Google Scholar
• Wang X, Liu J, Zheng Y et al. An optimized yeast cell-free system: sufficient for translation of human papillomavirus 58 L1 mRNA and assembly of virus-like particles. J. Biosci. Bioeng.106(1), 8–15 (2008).
   PubMed Web of Science ®Google Scholar
• Goshima N, Kawamura Y, Fukumoto A et al. Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat. Methods5(12), 1011–1017 (2008).
   PubMed Web of Science ®Google Scholar
• Hino M, Kataoka M, Kajimoto K et al. Efficiency of cell-free protein synthesis based on a crude cell extract from Escherichia coli, wheat germ, and rabbit reticulocytes. J. Biotechnol.133(2), 183–189 (2008).
   PubMed Web of Science ®Google Scholar
• Chandra H, Srivastava S. Cell-free synthesis-based protein microarrays and their applications. Proteomics10(4), 717–730 (2010).
   PubMed Web of Science ®Google Scholar
• Schwarz D, Dotsch V, Bernhard F. Production of membrane proteins using cell-free expression systems. Proteomics8(19), 3933–3946 (2008).
   PubMed Web of Science ®Google Scholar
• Katzen F, Peterson TC, Kudlicki W. Membrane protein expression: no cells required. Trends Biotechnol.27(8), 455–460 (2009).
   PubMed Web of Science ®Google Scholar
• He M. Cell-free protein synthesis: applications in proteomics and biotechnology. N. Biotechnol.25(2–3), 126–132 (2008).
   PubMed Web of Science ®Google Scholar
• Robinson WH. Antigen arrays for antibody profiling. Curr. Opin. Chem. Biol.10(1), 67–72 (2006).
   PubMed Web of Science ®Google Scholar
• Zhu H, Hu SH, Jona G et al. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proc. Natl Acad. Sci. USA103(11), 4011–4016 (2006).
   PubMed Web of Science ®Google Scholar
• Xu Y, Bruno JF, Luft BJ. Profiling the humoral immune response to Borrelia burgdorferi infection with protein microarrays. Microb. Pathog.45(5–6), 403–407 (2008).
   PubMed Web of Science ®Google Scholar
• Beare PA, Chen C, Bouman T et al. Candidate antigens for Q fever serodiagnosis revealed by immunoscreening of a Coxiella burnetii protein microarray. Clin. Vaccine Immunol.15(12), 1771–1779 (2008).
   PubMedGoogle Scholar
• Montor WR, Huang J, Hu Y et al. Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect. Immun.77(11), 4877–4886 (2009).
   PubMed Web of Science ®Google Scholar
• Doolan DL, Mu Y, Unal B et al. Profiling humoral immune responses to P. falciparum infection with protein microarrays. Proteomics8(22), 4680–4694 (2008).
   PubMed Web of Science ®Google Scholar
• Crompton PD, Kayala MA, Traore B et al. A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc. Natl Acad. Sci. USA107(15), 6958–6963 (2010).
   PubMed Web of Science ®Google Scholar
• Davies DH, Liang X, Hernandez JE et al. Profiling the humoral immune response to infection by using proteome microarrays: High-throughput vaccine and diagnostic antigen discovery. Proc. Natl Acad. Sci. USA102(3), 547–552 (2005).
   PubMed Web of Science ®Google Scholar
• Vigil A, Davies DH, Felgner PL. Defining the humoral immune response to infectious agents using high-density protein microarrays. Future Microbiol.5(2), 241–251 (2010).
   PubMed Web of Science ®Google Scholar
• Lueking A, Huber O, Wirths C et al. Profiling of alopecia areata autoantigens based on protein microarray technology. Mol. Cell Proteomics4(9), 1382–1390 (2005).
   PubMed Web of Science ®Google Scholar
• Hueber W, Kidd BA, Tomooka BH, Lee BJ. Antigen microarray profiling of autoantibodies in rheumatoid arthritis. Arthritis Rheum.52(9), 2645–2655 (2005).
   PubMed Web of Science ®Google Scholar
• Hueber W, Tomooka B, Batliwalla F et al. Blood autoantibody and cytokine profiles predict response to anti-tumor necrosis factor therapy in rheumatoid arthritis. Arthritis Res. Ther.11(3), R76 (2009).
   PubMed Web of Science ®Google Scholar
• Horn S, Lueking A, Murphy D et al. Profiling humoral autoimmune repertoire of dilated cardiomyopathy (DCM) patients and development of a disease-associated protein chip. Proteomics6(2), 605–613 (2006).
   PubMed Web of Science ®Google Scholar
• Quintana FJ, Farez MF, Viglietta V et al. Antigen microarrays identify unique serum autoantibody signatures in clinical and pathologic subtypes of multiple sclerosis. Proc. Natl Acad. Sci. USA105(48), 18889–18894 (2008).
   PubMed Web of Science ®Google Scholar
• Song Q, Liu G, Hu S et al. Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology. J. Proteome Res.9(1), 30–39 (2010).
   PubMed Web of Science ®Google Scholar
• Balboni I, Chan SM, Kattah M, Tenenbaum JD. Multiplexed protein array platforms for analysis of autoimmune diseases. Annu. Rev. Immunol.24, 391–418 (2006).
   PubMed Web of Science ®Google Scholar
• Chen G, Wang X, Yu J et al. Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma. Cancer Res.67(7), 3461–3467 (2007).
   PubMed Web of Science ®Google Scholar
• Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M. Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc. Natl Acad. Sci. USA104(44), 17494–17499 (2007).
   PubMed Web of Science ®Google Scholar
• Anderson KS, Ramachandran N, Wong J et al. Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer. J. Proteome Res.7(4), 1490–1499 (2008).
   PubMed Web of Science ®Google Scholar
• Babel I, Barderas R, Díaz-Uriarte R, Martínez-Torrecuadrada JL, Sánchez-Carbayo M, Casal JI. Identification of tumor-associated autoantigens for the diagnosis of colorectal cancer in serum using high density protein microarrays. Mol. Cell Proteomics8(10), 2382–2395 (2009).
   PubMed Web of Science ®Google Scholar
• Gnjatic S, Ritter E, Büchler MW et al. Seromic profiling of ovarian and pancreatic cancer. Proc. Natl Acad. Sci. USA107(11), 5088–5093 (2010).
   PubMed Web of Science ®Google Scholar
• Chatterjee M, Wojciechowski J, Tainsky MA. Discovery of antibody biomarkers using protein microarrays of tumor antigens cloned in high throughput. Methods Mol. Biol.520, 21–38 (2009).
   PubMedGoogle Scholar
• Kijanka G, Murphy D. Protein arrays as tools for serum autoantibody marker discovery in cancer. J. Proteomics72(6), 936–944 (2009).
   PubMed Web of Science ®Google Scholar
• Tan HT, Low J, Lim SG, Chung MC. Serum autoantibodies as biomarkers for early cancer detection. FEBS J.276(23), 6880–6904 (2009).
   PubMed Web of Science ®Google Scholar
• Caron M, Choquet-Kastylevsky GV, Joubert-Caron R. Cancer immunomics using autoantibody signatures for biomarker discovery. Mol. Cell Proteomics6(7), 1115–1122 (2007).
   PubMed Web of Science ®Google Scholar
• Zhang J-Y, Tan EM. Autoantibodies to tumor-associated antigens as diagnostic biomarkers in hepatocellular carcinoma and other solid tumors. Expert Rev. Mol. Diag.10(3), 321–328 (2010).
   PubMed Web of Science ®Google Scholar
• Wang X, Yu J, Sreekumar A et al. Autoantibody signatures in prostate cancer. N. Engl. J. Med.353(12), 1224–1235 (2005).
   PubMed Web of Science ®Google Scholar
• Qiu J, Choi G, Li L et al. Occurrence of autoantibodies to annexin I, 14–13-3 τ and LAMR1 in prediagnostic lung cancer sera. J. Clin. Oncol.26(31), 5060–5066 (2008).
   PubMed Web of Science ®Google Scholar
• Gibson DS, Banha J, Penque D et al. Diagnostic and prognostic biomarker discovery strategies for autoimmune disorders. J. Proteomics73(6), 1045–1060 (2010).
   PubMed Web of Science ®Google Scholar
• Kalbas M, Lueking A, Kowald A, Muellner S. New analytical tools for studying autoimmune diseases. Curr. Pharm. Des.12, 3735–3742 (2006).
   PubMed Web of Science ®Google Scholar
• Tozzoli R. Recent advances in diagnostic technologies and their impact in autoimmune diseases. Autoimmun. Rev.6(6), 334–340 (2007).
   PubMed Web of Science ®Google Scholar
• Andresen H, Grotzinger C. Deciphering the antibodyome – peptide arrays for serum antibody biomarker diagnostics. Curr. Proteomics6, 1–12 (2009).
   Google Scholar
• Prechl J, Papp KN, Erdei A. Antigen microarrays: descriptive chemistry or functional immunomics? Trends Immunol.31(4), 133–137 (2010).
   PubMed Web of Science ®Google Scholar
• Madi A, Hecht I, Bransburg-Zabary S et al. Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data. Proc. Natl Acad. Sci. USA106(34), 14484–14489 (2009).
   PubMed Web of Science ®Google Scholar
• He M, Stoevesandt O, Taussig MJ. In situ synthesis of protein arrays. Curr. Opin. Biotech.19(1), 4–9 (2008).
   PubMed Web of Science ®Google Scholar
• He M, Liu H, Turner M, Taussig MJ. Detection of protein–protein interactions by ribosome display and protein in situ immobilisation. N. Biotechnol.26(6), 277–281 (2009).
   PubMed Web of Science ®Google Scholar
• Ramachandran N, Raphael JV, Hainsworth E et al. Next-generation high-density self-assembling functional protein arrays. Nat. Methods5(6), 535–538 (2008).
   PubMed Web of Science ®Google Scholar
• He M, Stoevesandt O, Palmer EA et al. Printing protein arrays from DNA arrays. Nat. Methods5(2), 175–177 (2008).
   PubMed Web of Science ®Google Scholar
• Wong J, Sibani S, Lokko NN, LaBaer J, Anderson KS. Rapid detection of antibodies in sera using multiplexed self-assembling bead arrays. J. Immunol. Methods350(1–2), 171–182 (2009).
   PubMed Web of Science ®Google Scholar
• Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. Biomol. Eng.23(2–3), 77–88 (2006).
   PubMedGoogle Scholar
• Henderson G, Bradley M. Functional peptide arrays for high-throughput chemical biology based applications. Curr. Opin. Biotechnol.18(4), 326–330 (2007).
   PubMed Web of Science ®Google Scholar
• Hilpert K, Winkler DF, Hancock RE. Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat. Protoc.2(6), 1333–1349 (2007).
   PubMed Web of Science ®Google Scholar
• Poetz O, Ostendorp R, Brocks B et al. Protein microarrays for antibody profiling: specificity and affinity determination on a chip. Proteomics5(9), 2402–2411 (2005).
   PubMed Web of Science ®Google Scholar
• Chiari M, Cretich M, Corti A et al. Peptide microarrays for the characterization of antigenic regions of human chromogranin A. Proteomics5(14), 3600–3603 (2005).
   PubMed Web of Science ®Google Scholar
• Flinterman AE, Knol EF, Lencer DA et al. Peanut epitopes for IgE and IgG4 in peanut-sensitized children in relation to severity of peanut allergy. J. Allergy Clin. Immunol.121(3), 737–743 (2008).
   PubMed Web of Science ®Google Scholar
• Lottersberger J, Guerrero SA, Tonarelli GG et al. Epitope mapping of pathogenic Leptospira LipL32. Lett. Appl. Microbiol.49(5), 641–645 (2009).
   PubMed Web of Science ®Google Scholar
• Lin J, Bardina L, Shreffler WG et al. Development of a novel peptide microarray for large-scale epitope mapping of food allergens. J. Allergy Clin. Immunol.124(2), 315–322, 322 e1–3 (2009).
   PubMed Web of Science ®Google Scholar
• Larsson K, Eriksson C, Schwenk JM et al. Characterization of PrEST-based antibodies towards human cytokeratin-17. J. Immunol. Methods342(1–2), 20–32 (2009).
   PubMed Web of Science ®Google Scholar
• Hjelm B, Fernandez CD, Lofblom J et al. Exploring epitopes of antibodies toward the human tryptophanyl-tRNA synthetase. N. Biotechnol.27(2), 129–137 (2010).
   PubMed Web of Science ®Google Scholar
• Hilhorst R, Houkes L, van den Berg A, Ruijtenbeek R. Peptide microarrays for detailed, high-throughput substrate identification, kinetic characterization, and inhibition studies on protein kinase A. Anal. Biochem.387(2), 150–161 (2009).
   PubMed Web of Science ®Google Scholar
• Schutkowski M, Reimer U, Panse S et al. High-content peptide microarrays for deciphering kinase specificity and biology. Angew Chem. Int. Ed. Engl.43(20), 2671–2674 (2004).
   PubMed Web of Science ®Google Scholar
• Uttamchandani M, Yao SQ. Peptide microarrays: next generation biochips for detection, diagnostics and high-throughput screening. Curr. Pharm. Des.14, 2428–2438 (2008).
   PubMed Web of Science ®Google Scholar
• Breitling F, Felgenhauer T, Nesterov A et al. Particle-based synthesis of peptide arrays. Chembiochem.10(5), 803–808 (2009).
   PubMed Web of Science ®Google Scholar
• Breitling F, Nesterov A, Stadler V, Felgenhauer T, Bischoff FR. High-density peptide arrays. Mol. Biosyst.5(3), 224–234 (2009).
   PubMedGoogle Scholar
• Spurrier B, Honkanen P, Holway A et al. Protein and lysate array technologies in cancer research. Biotechnol. Adv.26(4), 361–369 (2008).
   PubMed Web of Science ®Google Scholar
• Paweletz C, Charboneau L, Bichsel V, Simone N. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene20(16), 1981–1989 (2001).
   PubMed Web of Science ®Google Scholar
• Hartmann M, Roeraade J, Stoll D, Templin MF, Joos TO. Protein microarrays for diagnostic assays. Anal. Bioanal. Chem.393(5), 1407–1416 (2009).
   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. USA100(24), 14229–14234 (2003).
   PubMed Web of Science ®Google Scholar
• Sheehan KM, Calvert VS, Kay EW et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell Proteomics4(4), 346–355 (2005).
   PubMed Web of Science ®Google Scholar
• Akkiprik M, Nicorici D, Cogdell D et al. Dissection of signaling pathways in fourteen breast cancer cell lines using reverse-phase protein lysate microarray. Technol. Cancer Res. Treat.5(6), 543–551 (2006).
   PubMed Web of Science ®Google Scholar
• Boyd ZS, Wu QJ, O’Brien C et al. Proteomic analysis of breast cancer molecular subtypes and biomarkers of response to targeted kinase inhibitors using reverse-phase protein microarrays. Mol. Cancer Ther.7(12), 3695–3706 (2008).
   PubMed Web of Science ®Google Scholar
• Janzi M, Ödling J, Pan-Hammarstrom Q et al. Serum microarrays for large scale screening of protein levels. Mol. Cell Proteomics4(12), 1942–1947 (2005).
   PubMed Web of Science ®Google Scholar
• Caiazzo Jr RJ, Maher AJ, Drummond MP et al. Protein microarrays as an application for disease biomarkers. Proteomics Clin. Appl., 3(2), 138–147 (2009).
   PubMed Web of Science ®Google Scholar
• Grote T, Siwak DR, Fritsche HA et al. Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19–9 levels in pancreatic cancer. Proteomics8(15), 3051–3060 (2008).
   PubMed Web of Science ®Google Scholar
• Aguilar-Mahecha A, Cantin C, O’Connor-McCourt M, Nantel A, Basik M. Development of reverse phase protein microarrays for the validation of clusterin, a mid-abundant blood biomarker. Proteome Sci.7, 15 (2009).
   PubMed Web of Science ®Google Scholar
• Srivastava M, Eidelman O, Jozwik C et al. Serum proteomic signature for cystic fibrosis using an antibody microarray platform. Mol. Genet. Metab.87(4), 303–310 (2006).
   PubMed Web of Science ®Google Scholar
• Mircean C, Shmulevich I, Cogdell D et al. Robust estimation of protein expression ratios with lysate microarray technology. Bioinformatics21(9), 1935–1942 (2005).
   PubMed Web of Science ®Google Scholar
• Janzi M, Sjöberg R, Wan J et al. Screening for C3 deficiency in newborns using microarrays. PLOS One4(4), e5321–e5321 (2009).
   PubMed Web of Science ®Google Scholar
• Janzi M, Kull I, Sjöberg R et al. Selective IgA deficiency in early life: association to infections and allergic diseases during childhood. Clin. Immunol.133(1), 78–85 (2009).
   PubMed Web of Science ®Google Scholar
• Hultschig C, Kreutzberger J, Seitz H et al. Recent advances of protein microarrays. Curr. Opin. Chem. Biol.10(1), 4–10 (2006).
   PubMed Web of Science ®Google Scholar
• Ramachandran N, Srivastava S, LaBaer J. Applications of protein microarrays for biomarker discovery. Proteomics Clin. Appl.2(10–11), 1444–1459 (2008).
   PubMed Web of Science ®Google Scholar
• Pawlak M, Schick E, Bopp MA et al. Zeptosens’ protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics2(4), 383–393 (2002).
   PubMed Web of Science ®Google Scholar
• Weissenstein U, Schneider MJ, Pawlak M et al. Protein chip based miniaturized assay for the simultaneous quantitative monitoring of cancer biomarkers in tissue extracts. Proteomics6(5), 1427–1436 (2006).
   PubMed Web of Science ®Google Scholar
• Oostrum Jv, Calonder C, Rechsteiner D et al. Tracing pathway activities with kinase inhibitors and reverse phase protein arrays. Proteomics Clin. Appl.3(4), 412–422 (2009).
   PubMed Web of Science ®Google Scholar
• Voshol H, Ehrat M, Traenkle J, Bertrand E, Oostrum JV. Antibody-based proteomics – analysis of signaling networks using reverse protein arrays. FEBS J.276(23), 6871–6879 (2009).
   PubMed Web of Science ®Google Scholar
• Pirnia F, Pawlak M, Thallinger GG et al. Novel functional profiling approach combining reverse phase protein microarrays and human 3-D ex vivo tissue cultures: expression of apoptosis-related proteins in human colon cancer. Proteomics9(13), 3535–3548 (2009).
   PubMed Web of Science ®Google Scholar
• Escher C, Lochmuller H, Fischer D et al. Reverse protein arrays as novel approach in muscular dystrophies. Neuromusc. Disord.20(5), 302–309 (2010).
   PubMed Web of Science ®Google Scholar
• Liumbruno G, D’Alessandro A, Grazzini G, Zolla L. Blood-related proteomics. J. Proteomics73(3), 483–507 (2010).
   PubMed Web of Science ®Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome – history, character, and diagnostic prospects. Mol. Cell Proteomics1(11), 845–867 (2002).
   PubMed Web of Science ®Google Scholar
• Anderson NL, Polanski M, Pieper R et al. The human plasma proteome – a nonredundant list developed by combination of four separate sources. Mol. Cell Proteomics3(4), 311–326 (2004).
   PubMed Web of Science ®Google Scholar
• Omenn GS, States DJ, Adamski M et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics5(13), 3226–3245 (2005).
   PubMed Web of Science ®Google Scholar
• States DJ, Omenn GS, Blackwell TW et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol.24(3), 333–338 (2006).
   PubMed Web of Science ®Google Scholar
• Mitchell BL, Yasui Y, Li CI, Fitzpatrick AL, Lampe PD. Impact of freeze–thaw cycles and storage time on plasma samples used in mass spectrometry based biomarker discovery projects. Cancer Inform.1, 98–104 (2005).
   PubMedGoogle Scholar
• Hsieh SY, Chen RK, Pan YH, Lee HL. Systematical evaluation of the effects of sample collection procedures on low-molecular-weight serum/plasma proteome profiling. Proteomics6(10), 3189–3198 (2006).
   PubMed Web of Science ®Google Scholar
• Alesci S, Borggrefe M, Dempfle C-E. Effect of freezing method and storage at -20°C and -70°C on prothrombin time, aPTT and plasma fibrinogen levels. Thrombosis Res.124(1), 121–126 (2009).
   PubMed Web of Science ®Google Scholar
• Gustaw KA, Garrett MR, Lee HG et al. Antigen–antibody dissociation in Alzheimer disease: a novel approach to diagnosis. J. Neurochem.106(3), 1350–1356 (2008).
   PubMed Web of Science ®Google Scholar
• Floriano PN, Christodoulides N, Miller CS et al. Use of saliva-based nano-biochip tests for acute myocardial infarction at the point of care: a feasibility study. Clin. Chem.55(8), 1530–1538 (2009).
   PubMed Web of Science ®Google Scholar
• Radziejewska I, Kisiel DG, Borzym-Kluczyk M et al. MUC 1 mucin content in gastric juice of duodenal ulcer patients: effect of Helicobacter pylori eradication therapy. Clin. Exp. Med.7(2), 72–76 (2007).
   PubMed Web of Science ®Google Scholar
• Spurr-Michaud S, Argueso P, Gipson I. Assay of mucins in human tear fluid. Exp. Eye Res.84(5), 939–950 (2007).
   PubMed Web of Science ®Google Scholar
• Sunita T, Dubey ML, Khurana S, Malla N. Specific antibody detection in serum, urine and saliva samples for the diagnosis of cystic echinococcosis. Acta Trop.101(3), 187–191 (2007).
   PubMed Web of Science ®Google Scholar
• Regeniter A, Kuhle J, Mehling M et al. A modern approach to CSF analysis: pathophysiology, clinical application, proof of concept and laboratory reporting. Clin. Neurol. Neurosurg.111(4), 313–318 (2009).
   PubMed Web of Science ®Google Scholar
• Johanson CE, Duncan JA 3rd, Klinge PM et al. Multiplicity of cerebrospinal fluid functions: new challenges in health and disease. Cerebrospinal Fluid Res.5, 10 (2008).
   PubMedGoogle Scholar
• Tsuji-Akimoto S, Yabe I, Niino M, Kikuchi S, Sasaki H. Cystatin C in cerebrospinal fluid as a biomarker of ALS. Neurosci. Lett.452(1), 52–55 (2009).
   PubMed Web of Science ®Google Scholar
• Somers V, Govarts C, Somers K et al. Autoantibody profiling in multiple sclerosis reveals novel antigenic candidates. J. Immunol.180(6), 3957–3963 (2008).
   PubMed Web of Science ®Google Scholar
• Dihazi H, Muller GA, Lindner S et al. Characterization of diabetic nephropathy by urinary proteomic analysis: identification of a processed ubiquitin form as a differentially excreted protein in diabetic nephropathy patients. Clin. Chem.53(9), 1636–1645 (2007).
   PubMed Web of Science ®Google Scholar
• Irmak S, Tilki D, Heukeshoven J et al. Stage-dependent increase of orosomucoid and zinc-α2-glycoprotein in urinary bladder cancer. Proteomics5(16), 4296–4304 (2005).
   PubMed Web of Science ®Google Scholar
• Theodorescu D, Wittke S, Ross MM et al. Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol.7(3), 230–240 (2006).
   PubMed Web of Science ®Google Scholar
• Theodorescu D, Schiffer E, Bauer HW et al. Discovery and validation of urinary biomarkers for prostate cancer. Proteomics Clin. Appl.2(4), 556–570 (2008).
   PubMed Web of Science ®Google Scholar
• Decramer S, Gonzalez de Peredo A, Breuil B et al. Urine in clinical proteomics. Mol. Cell Proteomics7(10), 1850–1862 (2008).
   PubMed Web of Science ®Google Scholar
• Barratt J, Topham P. Urine proteomics: the present and future of measuring urinary protein components in disease. CMAJ177(4), 361–368 (2007).
   PubMed Web of Science ®Google Scholar
• Schwenk JM, Stoll D, Templin MF, Joos TO. Cell microarrays: an emerging technology for the characterization of antibodies. Biotechniques (Suppl.) 54–61 (2002).
   PubMedGoogle Scholar
• Hart T, Zhao A, Garg A, Bolusani S, Marcotte EM. Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays. PLOS One4(10), e7088 (2009).
   PubMed Web of Science ®Google Scholar
• Stromberg S, Bjorklund MG, Asplund C et al. A high-throughput strategy for protein profiling in cell microarrays using automated image analysis. Proteomics7(13), 2142–2150 (2007).
   PubMed Web of Science ®Google Scholar
• Kononen J, Bubendorf L, Kallioniemi A et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med.4(7), 844–847 (1998).
   PubMed Web of Science ®Google Scholar
• Xu BJ. Combining laser capture microdissection and proteomics: methodologies and clinical applications. Proteom. Clin. Appl.4(2), 116–123 (2010).
   PubMed Web of Science ®Google Scholar
• Knezevic V, Leethanakul C, Bichsel VE et al. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics1(10), 1271–1278 (2001).
   PubMed Web of Science ®Google Scholar
• Barelli S, Crettaz D, Thadikkaran L, Rubin O, Tissot JD. Plasma/serum proteomics: pre-analytical issues. Expert Rev. Proteomics4(3), 363–370 (2007).
   PubMed Web of Science ®Google Scholar
• Bjorhall K, Miliotis T, Davidsson P. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics5(1), 307–317 (2005).
   PubMed Web of Science ®Google Scholar
• Whiteaker JR, Zhang H, Eng JK et al. Head-to-head comparison of serum fractionation techniques. J. Proteome Res.6(2), 828–836 (2007).
   PubMed Web of Science ®Google Scholar
• Pernemalm M, Lewensohn R, Lehtio J. Affinity prefractionation for MS-based plasma proteomics. Proteomics9(6), 1420–1427 (2009).
   PubMed Web of Science ®Google Scholar
• Roche S, Tiers L, Provansal M et al. Depletion of one, six, twelve or twenty major blood proteins before proteomic analysis: the more the better? J. Proteomics72(6), 945–951 (2009).
   PubMed Web of Science ®Google Scholar
• Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J. Sep. Sci.32(5–6), 771–798 (2009).
   PubMed Web of Science ®Google Scholar
• Polaskova V, Kapur A, Khan A, Molloy MP, Baker MS. High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis31(3), 471–482 (2010).
   PubMed Web of Science ®Google Scholar
• Fang XM, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J. Proteomics71(3), 284–303 (2008).
   PubMed Web of Science ®Google Scholar
• Geiger T, Cox J, Ostasiewicz P, Wisniewski JR, Mann M. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat. Methods7(5), 383–385 (2010).
   PubMed Web of Science ®Google Scholar
• Zielinska DF, Gnad F, Wisniewski JR, Mann M. Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell141(5), 897–907 (2010).
   PubMed Web of Science ®Google Scholar
• Tibes R, Qiu Y, Lu Y et al. Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther.5(10), 2512–2521 (2006).
   PubMed Web of Science ®Google Scholar
• Rimini R, Schwenk JM, Sundberg M et al. Validation of serum protein profiles by a dual antibody array approach. J. Proteomics73(2), 252–266 (2009).
   PubMed Web of Science ®Google Scholar
• Kricka LJ, Master SR. Validation and quality control of protein microarray-based analytical methods. Mol. Biotechnol.38(1), 19–31 (2008).
   PubMed Web of Science ®Google Scholar
• Chen C, McGarvey PB, Huang H, Wu CH. Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput ‘omics’ data. Adv. Bioinformatics2010, 1–20 (2010).
   Google Scholar
• Kricka LJ, Master SR. Quality control and protein microarrays. Clin. Chem.55(6), 1053–1055 (2009).
   PubMed Web of Science ®Google Scholar
• Yang HN, Harrington CA, Vartanian K et al. Randomization in laboratory procedure is key to obtaining reproducible microarray results. PLOS One3(11), e3724 (2008).
   Google Scholar
• Filzmoser P, Maronna R, Werner M. Outlier identification in high dimensions. Comput. Stat. Data Anal.52(3), 1694–1711 (2008).
   Web of Science ®Google Scholar
• Shieh AD, Hung YS. Detecting outlier samples in microarray data. Stat. Appl. Genet. Mol. Biol.8(1), Article 13 (2009).
   PubMed Web of Science ®Google Scholar
• Schulz-Trieglaff O, Machtejevas E, Reinert K et al. Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min.2(1), 4 (2009).
   PubMed Web of Science ®Google Scholar
• van den Berg RA, Hoefsloot HCJ, Westerhuis JA, Smilde AK, van der Werf MJ. Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics7, 142 (2006).
   PubMed Web of Science ®Google Scholar
• Sboner A, Karpikov A, Chen G et al. Robust-linear-model normalization to reduce technical variability in functional protein microarrays. J. Proteome Res.9(1), 636–636 (2009).
   Google Scholar
• Hamelinck D, Zhou H, Li L et al. Optimized normalization for antibody microarrays and application to serum-protein profiling. Mol. Cell Proteomics4(6), 773–784 (2005).
   PubMed Web of Science ®Google Scholar
• Cohen Freue GV, Hollander Z, Shen E et al. MDQC: a new quality assessment method for microarrays based on quality control reports. Bioinformatics23(23), 3162–3169 (2007).
   PubMed Web of Science ®Google Scholar
• Dieterle F, Ross A, Schlotterbeck G, Senn H. Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal. Chem.78(13), 4281–4290 (2006).
   PubMed Web of Science ®Google Scholar
• Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol.3, Article 3 (2004).
   Google Scholar
• Corzett TH, Fodor IK, Choi MW et al. Statistical analysis of variation in the human plasma proteome. J. Biomed. Biotechnol.2010, 258494 (2010).
   PubMedGoogle Scholar
• Daly DS, Anderson KK, Seurynck-Servoss SL et al. An internal calibration method for protein-array studies. Stat. Appl. Genet. Mol. Biol.9(1), Article 14 (2010).
   PubMed Web of Science ®Google Scholar
• Silva-Aycaguer LC, Suarez-Gil P, Fernandez-Somoano A. The null hypothesis significance test in health sciences research (1995–2006): statistical analysis and interpretation. BMC Med. Res. Methodol.10(1), 44 (2010).
   PubMed Web of Science ®Google Scholar
• Reiner A. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics19(3), 368–375 (2003).
   PubMed Web of Science ®Google Scholar
• Graf AC, Bauer P. Model selection based on FDR-thresholding optimizing the area under the ROC-curve. Stat. Appl. Genet. Mol. Biol.8(1), Article 31 (2009).
   Google Scholar
• Noble WS. How does multiple testing correction work? Nat. Biotechnol.27(12), 1135–1137 (2009).
   PubMed Web of Science ®Google Scholar
• Tang Y, Zhang Y-Q, Huang Z. Development of two-stage SVM-RFE gene selection strategy for microarray expression data analysis. IEEE/ACM Trans. Comput. Biol. Bioinform.4(3), 365–381 (2007).
   PubMed Web of Science ®Google Scholar
• Zhang J, Wang Y, Dong Y, Wang Y. Ultrasonographic feature selection and pattern classification for cervical lymph nodes using support vector machines. Comput. Methods Programs Biomed.88(1), 75–84 (2007).
   PubMed Web of Science ®Google Scholar
• Zhang X, Lu X, Shi Q et al. Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics7, 197 (2006).
   PubMed Web of Science ®Google Scholar
• Hartmann M, Schrenk M, Döttinger A et al. Expanding assay dynamics: a combined competitive and direct assay system for the quantification of proteins in multiplexed immunoassays. Clin. Chem.54(6), 956–963 (2008).
   PubMed Web of Science ®Google Scholar
• Ocana MF, Neubert H. An immunoaffinity liquid chromatography-tandem mass spectrometry assay for the quantitation of matrix metalloproteinase 9 in mouse serum. Anal. Biochem.399(2), 202–210 (2010).
   PubMed Web of Science ®Google Scholar
• James J, Moresco PCC, Yates JR III. Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry. J. Proteomics73(11), 2198–2204 (2010).
   PubMed Web of Science ®Google Scholar
• Poetz O, Luckert K, Herget T, Joos T. Microsphere-based co-immunoprecipitation next term in multiplex. Anal. Biochem.395(2), 244–248 (2009).
   PubMed Web of Science ®Google Scholar
• Cheng D, Branscum AJ, Stamey JD. Accounting for response misclassification and covariate measurement error improves power and reduces bias in epidemiologic studies. Ann. Epidemiol.20(7), 562–567 (2010).
   PubMed Web of Science ®Google Scholar
• Casal JI, Barderas R. Identification of cancer autoantigens in serum: toward diagnostic/prognostic testing? Mol. Diagn. Ther.14(3), 149–154 (2010).
   PubMed Web of Science ®Google Scholar
• Riegman PH, Dinjens WN, Oosterhuis JW. Biobanking for interdisciplinary clinical research. Pathobiology74(4), 239–244 (2007).
   PubMed Web of Science ®Google Scholar
• Riegman PH, Morente MM, Betsou F, de Blasio P, Geary P. Biobanking for better healthcare. Mol. Oncol.2(3), 213–222 (2008).
   PubMed Web of Science ®Google Scholar
• Jackson DH, Banks RE. Banking of clinical samples for proteomic biomarker studies: a consideration of logistical issues with a focus on pre-analytical variation. Proteom. Clin. Appl.4(3), 250–270 (2010).
   PubMed Web of Science ®Google Scholar
• Owen JM, Woods P. Designing and implementing a large-scale automated -80 degrees C archive. Int. J. Epidemiol.37(Suppl. 1), I56–I61 (2008).
   PubMed Web of Science ®Google Scholar
• Downey P, Peakman TC. Design and implementation of a high-throughput biological sample processing facility using modern manufacturing principles. Int. J. Epidemiol.37, 46–50 (2008).
   PubMed Web of Science ®Google Scholar
• Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature452(7187), 571–579 (2008).
   PubMed Web of Science ®Google Scholar
• Uhlen M. Mapping the human proteome using antibodies. Mol. Cell Proteomics6(8), 1455–1456 (2007).
   PubMed Web of Science ®Google Scholar