Antibodypedia, a portal for sharing antibody and antigen validation data.
ABSTRACT Antibodies are useful tools to characterize the components of the human proteome and to validate potential protein biomarkers discovered through various clinical proteomics efforts. The lack of validation results across various applications for most antibodies often makes it necessary to perform cumbersome investigations to ensure specificity of a particular antibody in a certain application. A need therefore exists for a standardized system for sharing validation data about publicly available antibodies and to allow antibody providers as well as users to contribute and edit experimental evidence data, including data also on the antigen. Here we describe a new publicly available portal called Antibodypedia, which has been developed to allow sharing of information regarding validation of antibodies in which providers can submit their own validation results and reliability scores. We report standardized validation criteria and submission rules for applications such as Western blots, protein arrays, immunohistochemistry, and immunofluorescence. The contributor is expected to provide experimental evidence and a validation score for each antibody, and the users can subsequently provide feedback and comments on the use of the antibody. The database thus provides a virtual resource of publicly available antibodies toward human proteins with accompanying experimental evidence supporting an individual validation score for each antibody in an application-specific manner.
Article: Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies.[show abstract] [hide abstract]
ABSTRACT: Antibody microarrays have the potential to enable comprehensive proteomic analysis of small amounts of sample material. Here, protocols are presented for the production, quality assessment, and reproducible application of antibody microarrays in a two-color mode with an array of 1,800 features, representing 810 antibodies that were directed at 741 cancer-related proteins. In addition to measures of array quality, we implemented indicators for the accuracy and significance of dual-color detection. Dual-color measurements outperform a single-color approach concerning assay reproducibility and discriminative power. In the analysis of serum samples, depletion of high-abundance proteins did not improve technical assay quality. On the contrary, depletion introduced a strong bias in protein representation. In an initial study, we demonstrated the applicability of the protocols to proteins derived from urine samples. We identified differences between urine samples from pancreatic cancer patients and healthy subjects and between sexes. This study demonstrates that biomedically relevant data can be produced. As demonstrated by the thorough quality analysis, the dual-color antibody array approach proved to be competitive with other proteomic techniques and comparable in performance to transcriptional microarray analyses.Molecular & Cellular Proteomics 02/2010; 9(6):1271-80. · 7.40 Impact Factor
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ABSTRACT: The process for data collection in multicenter trials may be troublesome and expensive. We report our experience with the spreadsheet function in Googledocs for this purpose. In Googledocs the data manager creates a form similar to the paper case record form, which will function as a decentral data entry module. When the forms are submitted, they are presented in a spreadsheet in Googledocs, which can be exported to different standard spreadsheet formats. For a multicenter randomized clinical trial with five different participating hospitals we created a decentral data entry module using the spreadsheet function in Googledocs. The study comprised 332 patients (clinicaltrials.gov identifier: NCT00815698) with five visits per patient. One person at each study site entered data from the original paper based case report forms which were kept at the study sites as originals. We did not experience any technical problems using the system. The system allowed for decentral data entry, and it was easy to use, safe, and free of charge. The spreadsheet function in Googledocs may potentially replace current expensive solutions for data acquisition in multicenter trials. clinicaltrials.gov NCT00815698.Trials 01/2010; 11:49. · 2.02 Impact Factor
Article: Phage display for the generation of antibodies for proteome research, diagnostics and therapy.[show abstract] [hide abstract]
ABSTRACT: Twenty years after its development, antibody phage display using filamentous bacteriophage represents the most successful in vitro antibody selection technology. Initially, its development was encouraged by the unique possibility of directly generating recombinant human antibodies for therapy. Today, antibody phage display has been developed as a robust technology offering great potential for automation. Generation of monospecific binders provides a valuable tool for proteome research, leading to highly enhanced throughput and reduced costs. This review presents the phage display technology, application areas of antibodies in research, diagnostics and therapy and the use of antibody phage display for these applications.Molecules 01/2011; 16(1):412-26. · 2.39 Impact Factor