Proteins are dynamic molecules; they undergo crucial conformational changes induced by post-translational modifications and by binding of cofactors or other molecules. The characterization of these conformational changes and their relation to protein function is a central goal of structural biology. Unfortunately, most conventional methods to obtain structural information do not provide information on protein dynamics. Therefore, mass spectrometry-based approaches such as limited proteolysis, hydrogen-deuterium exchange and stable-isotope labeling are nowadays frequently used to characterize protein conformation and dynamics. Yet the interpretation of these data can be cumbersome and time-consuming. Here, we present PepShell, a tool that allows interactive data analysis of mass spectrometry-based conformational proteomics studies by visualization of the identified peptides both at the sequence and at the structure level. Moreover, PepShell allows the comparison of experiments under different conditions including different proteolysis times or binding of the protein to different substrates or inhibitors.