The rapid progresses of high throughput mass spectrometry (MS)-based proteomics such as data-independent acquisition (DIA) and its penetration to clinical studies have generated increasing number of proteomic data sets containing 100s-1000s samples. To analyze these big proteomic data sets more efficiently and conveniently, we present a web server-based software tool ProteomeExpert implemented in Docker, which offers various analysis tools for experimental design, data mining, interpretation, and visualization of big proteomic data sets. ProteomeExpert can be deployed on an operating system with Docker installed.