Analytical Platforms 3: Processing Samples via the RPPA Pipeline to Generate Large-Scale Data for Clinical Studies

Reverse phase protein array (RPPA) is a functional proteomics technology amenable to moderately high throughputs of samples and antibodies. The University of Texas MD Anderson Cancer Center RPPA Core Facility has implemented various processes and techniques to maximize RPPA throughput; key among them are maximizing array configuration and relying on database management and automation. One major tool used by the RPPA Core is a semi-automated RPPA process management system referred to as the RPPA Pipeline. The RPPA Pipeline, developed with the aid of MD Avnderson's Department of Bioinformatics and Computational Biology and InSilico Solutions, has streamlined sample and antibody tracking as well as advanced quality control measures of various RPPA processes. This chapter covers RPPA Core processes associated with the RPPA Pipeline workflow from sample receipt to sample printing to slide staining and RPPA report generation that enables the RPPA Core to process at least 13,000 samples per year with approximately 450 individual RPPA-quality antibodies. Additionally, this chapter will cover results of large-scale clinical sample processing, including The Cancer Genome Atlas Project and The Cancer Proteome Atlas.