Value of the data •We present a benchmarking dataset to evaluate tools, analysis methods and visualizations for the dynamic epiproteome. The phosphosites in this dataset are well studied - they have been the subject of multiple prior publications. •We provide these data converted into the required input formats for four currently available tools. These files can be used to recreate visualizations discussed in the originating paper. •We provide a small kappa model on the subject of these phosphosites. Models such as these can be used to validate our understanding of the processes in the underlying cellular system.