The plot might become pretty crowded if multiple peaks are close to each other though. Anyway:

spec = spec.scale_intensity(max_intensity=1)
for fragment_mz, fragment_in in zip(spec.mz, spec.intensity):
    if fragment_in >= 0.05:
        spec.annotate_mz_fragment(fragment_mz, None, 0.1, 'Da')

If you select the most intense peak within a certain window (e.g. 10 mz, or scale the window with the max(mz) so it's a larger window for higher mz spectra) for annotation, you will be able to avoid most overlap automatically, but still be informative (at least those values are what worked for us in R). Depends how you wish to orient the text. I piggybacked off the satellite peak filtering in RMassBank:
https://github.com/schymane/ReSOLUTION/blob/master/R/MS1_functions.R#L115

I could easily implement Emma's suggestion within the app...

Done - it's a bit messy, but we can tidy up.

• Plots just 2dp of mz
• Doesn't plot things too close in mz to one another
• Width (for exclusion) is calculated based upon min and max mz range to ensure zoomed in regions can still get plenty of labels

Can we have 4 dp please? Or an option to add more than 2? It's essential for interpretation.