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

Area of Science:

• Proteomics
• Functional Proteomics
• Biotechnology

Background:

• Reverse phase protein array (RPPA) is a functional proteomics technique.
• High-throughput sample and antibody processing is crucial for large-scale studies.
• Existing RPPA workflows require optimization for efficiency and data management.

Purpose of the Study:

• To describe the RPPA Pipeline, a semi-automated system for managing RPPA processes.
• To detail the workflow from sample receipt to report generation.
• To highlight the system's capacity for high-throughput clinical sample processing.

Main Methods:

• Implementation of a semi-automated RPPA process management system (RPPA Pipeline).
• Maximizing array configuration and utilizing database management and automation.
• Streamlining sample and antibody tracking and implementing advanced quality control.

Main Results:

• The RPPA Pipeline enables processing of at least 13,000 samples per year with approximately 450 antibodies.
• The system streamlines sample tracking, printing, staining, and report generation.
• Successful large-scale clinical sample processing, including TCGA and TCPA projects.

Conclusions:

• The RPPA Pipeline significantly enhances throughput and efficiency in functional proteomics.
• The system supports large-scale clinical sample analysis for cancer research initiatives.
• Database management and automation are key to maximizing RPPA Core facility capacity.