title: ProMAT calibrator: A tool for reducing experimental bias in antibody microarrays.
abstract: Our research group has been developing enzyme-linked immunosorbent assays (ELISA) microarray technology for the rapid and quantitative evaluation of biomarker panels. Studies using antibody microarrays are susceptible to systematic bias from the various steps in the experimental process, and these biases can mask biologically significant differences. For this reason, we have developed a calibration system that can identify and reduce systematic bias due to processing factors. Specifically, we developed a sandwich ELISA for green fluorescent protein (GFP) that is included on each chip. The GFP antigen is spiked into each biological sample or standard mixture and the resulting signal is used for calibration between chips. We developed ProMAT Calibrator, an open-source bioinformatics tool, for the rapid visualization and interpretation of the calibrator data and, if desired, data normalization. We demonstrate that data normalization using this system markedly reduces bias from processing factors. Equally useful, this calibrator system can help reveal the source of the bias, thereby facilitating the elimination of the underlying problem. ProMAT Calibrator can be downloaded at http://www.pnl.gov/statistics/ProMAT .
authors.affiliation: Pacific Northwest National Laboratory, Richland, Washington 99354, USA. richard.zangar@pnl.gov
authors.forename: R C
authors.initials: RC
authors.lastname: Zangar
authors.forename: D S
authors.initials: DS
authors.lastname: Daly
authors.forename: A M
authors.initials: AM
authors.lastname: White
authors.forename: S L
authors.initials: SL
authors.lastname: Servoss
authors.forename: R M
authors.initials: RM
authors.lastname: Tan
authors.forename: J R
authors.initials: JR
authors.lastname: Collett
mesh_terms: D000906:Antibodies / Q000032:analysis* / Q000378:metabolism; D000941:Antigens / Q000378:metabolism; D002138:Calibration; D004797:Enzyme-Linked Immunosorbent Assay / Q000379:methods; D049452:Green Fluorescent Proteins / Q000032:analysis / Q000737:chemistry; D016015:Logistic Models; D040081:Protein Array Analysis / Q000379:methods* / Q000592:standards; D040901:Proteomics / Q000379:methods* / Q000592:standards; D012984:Software
chemical_list: D000906:Antibodies; D000941:Antigens; D049452:Green Fluorescent Proteins