Generation of Raw RPPA Data and Their Conversion to Analysis-Ready Data.

Reverse phase protein array (RPPA) provides investigators with a powerful high-throughput, quantitative, cost-effective technology for functional proteomics studies. It is an antibody-based technique with procedures similar to that of Western blots. RPPA has a wide variety of applications that range from pharmacodynamics and drug sensitivity assessment to biomarker discovery, subtype classification, and prediction of patient prognosis and response to targeted therapy. In this paper, we describe the technology, its limitations, and some solutions to overcome them. We discuss the steps necessary to obtain raw RPPA data and convert them into robust, high-quality, analysis-ready data. We then illustrate the utility of the platform by highlighting some biomarkers and drug responses of cancer cell lines that confirm previous findings, as a means to validate the platform and the methods presented here.