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The Chromosome-centric Human Proteome Project (C-HPP) aims to map and annotate the entire human proteome by the “chromosome-by-chromosome” strategy. As the C-HPP proceeds, the increasing volume of proteomic data sets presents a challenge for customized and reproducible bioinformatics data analyses for mining biological knowledge. To address this challenge, we updated the previous static proteome browser CAPER into a higher version, CAPER 2.0 – an interactive, configurable and extensible workflow-based platform for C-HPP data analyses. In addition to the previous visualization functions of track-view and heatmap-view, CAPER 2.0 presents a powerful toolbox for C-HPP data analyses and also integrates a configurable workflow system that supports the view, construction, edit, run, and share of workflows. These features allow users to easily conduct their own C-HPP proteomic data analyses …