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Repeatedly identified differentially expressed proteins (RIDEPs) from antibody microarray proteomic analysis

Hodgkinson, Victoria C.; ELFadl, Dalia; Drew, Philip J.; Lind, Michael J.; Cawkwell, Lynn

Authors

Victoria C. Hodgkinson

Dalia ELFadl

Philip J. Drew

Professor Michael Lind M.J.Lind@hull.ac.uk
Foundation Professor of Oncology/ Head of the Joint Centre for Cancer Studies

Abstract

Antibody microarrays are powerful new tools in the field of comparative proteomics. The success of the biomarker discovery pipeline relies on the quality of data generated in the discovery phase and careful selection of proteins for the verification phase. Recent meta-analyses found a number of repeatedly identified differentially expressed proteins (RIDEPs) from mass spectrometry-based proteomics research in a range of species. We aimed to assess RIDEPs based on antibody microarray data-sets. A total of 13 independent experiments encompassing a range of oncology-related research on human tissue, cells or cell lines from 5 distinct sample groups were performed utilising a commercial 725 antibody microarray platform (Panorama XPRESS Profiler725; Sigma-Aldrich). Analysis of all microarray slides was carried out by the same individual to reduce inter-observer variability. Fold changes of >= 1.8 were considered significant. A total of 13 RIDEPs were seen, each appearing in at least 4/13 (30%) antibody microarray analyses from at least 2 out of 5 experimental sample groups. The phenomenon of RIDEPs may exist in antibody microarray proteomics and we report a preliminary list of 13 RIDEPs from the XPRESS Profiler725 platform. This information will be useful when interpreting experimental data and considering which DEPs should be prioritised for verification. (C) 2011 Elsevier B.V. All rights reserved.

Journal Article Type Article
Publication Date May 1, 2011
Journal JOURNAL OF PROTEOMICS
Print ISSN 1874-3919
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 74
Issue 5
Pages 698-703
Institution Citation Hodgkinson, V. C., ELFadl, D., Drew, P. J., Lind, M. J., & Cawkwell, L. (2011). Repeatedly identified differentially expressed proteins (RIDEPs) from antibody microarray proteomic analysis. Journal of Proteomics, 74(5), (698-703). doi:10.1016/j.jprot.2011.02.014. ISSN 1874-3919
DOI https://doi.org/10.1016/j.jprot.2011.02.014
Keywords Antibody microarray; Biomarkers; Differentially expressed proteins; Protein expression; Proteomics