Overview of QUDeX-MS possible workflows. QUDeX-MS can be launched either from MATLAB or as a standalone executable. Once loaded, a Command Window (top right) and Spectrum View window (bottom) appear. Spectra can be loaded one at a time, with all loaded spectra managed in the Loaded Spectra listbox. The active spectrum selected in the Loaded Spectra listbox will be displayed in the Spectrum Viewer window. After loading a spectrum to analyze, several routes can be chosen for estimating deuterium incorporation of ion signals in the spectrum. An ion can be selected for analysis either by specifying a formula (or peptide sequence), locating a distribution in the spectrum, or specifying a monoisotopic m/z. Once an ion is loaded, it is displayed in the Loaded Ion listbox, and a deuterium incorporation distribution can be determined from the selected spectrum by selecting Calculate Exchange. Specific deuterium-associated peaks can be selected from the Command Window to quickly navigate to a zoomed view of their region of the spectrum in the Spectrum Viewer. If the elemental formula has been specified, the distribution of deuterium incorporation can then be used to calculate a theoretical spectrum by selecting Model Spectrum. A calculated isotopic fine structure line spectrum will then be displayed over the loaded spectrum in the Spectrum Viewer window.