Summary: Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming increasing routine for monitoring changes in the structural dynamics of proteins. Differential HDX-MS allows comparison of individual protein states, such as in the absence or presence of a ligand. This can be used to attribute changes in conformation to binding events, allowing the mapping of entire con-formational networks. As such, the number of necessary cross-state comparisons quickly increas-es as additional states are introduced to the system of study. There are currently very few software packages available that offer quick and informative comparison of HDX-MS datasets and even few-er which offer statistical analysis and advanced visualization. Following the feedback from our origi-nal software Deuteros, we present Deuteros 2.0 which has been redesigned from the ground up to fulfil a greater role in the HDX-MS analysis pipeline. Deuteros 2.0 features a repertoire of facilities for back exchange correction, data summarization, peptide-level statistical analysis and advanced data plotting features. Availability: Deuteros 2.0 can be downloaded from https://github.com/andymlau/Deuteros_2.0 under the Apache 2.0 license. Installation of Deuteros 2.0 requires the MATLAB Runtime Library available free of charge from MathWorks (https://www.mathworks.com/products/compiler/matlab-runtime.html) and is available for both Windows and Mac operating systems.