Hydrogen-deuterium mass spectrometry (HDX-MS) is an analytical tool for monitoring dynamics and interactions of proteins. In the glaring opposite to crystallography-based methods, HDX-MS allows a unique insight into the dynamics of the protein structure. Such data is larger and more complicated than static structure, thus requires a dedicated software suite that is provided by a few vendors. However, the majority of existing tools do not cover a complete analytic workflow, especially on the level of data presentation and proper statistical interpretation. We propose HaDeX, a novel tool for processing, analysis, and visualization of output data from existing search engines used in HDX-MS experiments. HaDeX features functions supporting the whole analytical process, including preliminary data exploration, ISO-based uncertainty, quality control, and generation of publication-quality figures. The reproducibility of the entire procedure is ensured with advanced reporting functions. HaDeX is available primarily as a web-server (http://mslab-ibb.pl/shiny/HaDeX/), but all functionalities are also accessible as the R package and standalone software.