A few questions before I give one possible solution,
Does this plot need to be updated in real time ? or is this plot to be done in post processing?
if you can do the plots with post processing you should be able to use pcolor function to do your tasks
i won’t go into details but just assign:
X as 1d vector with your m/z values
Y as 1d vector your time values
And Z as a 2d array that will map counts/sec to both a “m/z” and “time” index
You will have to find the location for your other marks and then plot them on top of pcolor graph but that shouldn’t be too hard just express your values (i am assuming 3dB cutoff points and peak power of some sort) in terms of X Y. I am almost certain there is probably a nice DSP way to solve for those X Y values once the data is in a 2d array but i am no expert on that mater.
Good luck and hopefully this helps,