Abstract
SummaryHydrogen 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 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 conformational networks. As such, the number of necessary cross-state comparisons quickly increases 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 fewer which offer statistical analysis and advanced visualization. Following the feedback from our original software Deuteros, we present Deuteros 2.0 which has been redesigned from the ground up to fulfill 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 and implementationDeuteros 2.0 can be downloaded for both Windows and MacOS from https://github.com/andymlau/Deuteros_2.0 under the Apache 2.0 license.
Highlights
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a structural MS technique which can be used to monitor changes in both protein structure and conformation (Marcsisin and Engen, 2010)
HDX-MS experiments are commonly performed in a differential manner which envisions that two or more datasets collected from the same protein but in different conditions are compared with one another to study changes in regional deuterium uptake as a function of environmental changes
Raw data acquired from HDX-MS must undergo several processing steps before it can be interpreted (Claesen and Burzykowski, 2017; Wales, et al, 2013)
Summary
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a structural MS technique which can be used to monitor changes in both protein structure and conformation (Marcsisin and Engen, 2010). HDX-MS experiments are commonly performed in a differential manner which envisions that two or more datasets collected from the same protein but in different conditions are compared with one another to study changes in regional deuterium uptake as a function of environmental changes. Such changes can include the addition of interacting species such as substrates or even modifications to the target protein itself (Martens, et al, 2018). Parallel to developments in the HDX-MS field, we present here Deuteros 2.0 which has been redesigned from the ground up with new features intended to further streamline the analysis of HDX-MS data
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