Large scale sample management and data analysis via MIRACLE

Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. In the past years the technology advanced based on improved methods and protocols concerning sample preparation and printing, antibody selection, optimization of staining conditions and mode of signal analysis. However, the sample management and data analysis still poses challenges because of the high number of samples, sample dilutions, customized array patterns, and various programs necessary for array construction and data processing.
We developed a comprehensive and user-friendly web application called MIRACLE (MIcroarray R-based Analysis of Complex Lysate Experiments), which bridges the gap between sample management and array analysis by conveniently keeping track of the sample information from lysate preparation, through array construction and signal evaluation. Subsequent data analysis may include correction of unequal array staining (surface normalization), estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists a customized end-to-end solution for sample management and for data analysis. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis.