Seems that in this example of an extracted spectrum, when binning is turned on there is a big shift in the m/z (by 2 Da). Code: https://pyopenms-viz.readthedocs.io/en/latest/gallery/ms_bokeh/plot_spectrum_dia_ms_bokeh.html Add bin_peaks = False  Add nothing (bin_peaks = True)  Top image is what expect from dataframe. Note: I am working on branch https://github.com/OpenMS/pyopenms_viz/pull/39 so I am not sure if issue is coming from there.