<p dir="ltr">This dataset contains mass spectra (.raw) and mass spectrometry imaging (MSI) data (.imzML) from a deuterium isotope labeling experiment. The ‘.imzML files’ are used to generate MS images using MSiReader. The data files are split across four folders, along with a separate .xlsx analysis file, which correspond to the accompanying article, "Mass spectrometry imaging of <i>Arabidopsis thaliana</i> with <i>in vivo</i> D<sub>2</sub>O labeling." This study demonstrates that MSI<i>i</i> can reveal spatiotemporal metabolic activities in various tissues of the <i>A. thaliana</i> plant.</p>