A benchmark dataset for analyzing and visualizing the dynamic epiproteome

In this paper, we present a benchmark dataset to evaluate the currently available analysis methods and visualizations for epiproteomic data. The benchmark dataset is a subset of a high-throughput time-series study of phosphoevents occurring upon insulin stimulation. Our dataset is provided in multiple formats for use with four currently available tools. We also provide a file containing the kinase assignments for the sites, as well as a simple kappa model on phosphorylation changes in insulin signalling. A detailed description of the tools, their analysis methods, and the visualizations generated using the input files described here, are discussed in detail in the accompanying review titled “Visualization and analysis of epiproteome dynamics" [1].