Unzooming a MS/MS spectrum at this point is fairly painful, as the colord bands disappear and all the labels remain at the top of the graph, where they overlap each other and become mostly unreadable.

We should have some zoom threshold (once the colored band becomes uninformative), where we drop them from the top of the graph to just above the maximum intensity they are labeling (as in the Library Match pane), and we should make sure that at least one 2-pixel strip of the color of the transition they are measuring remains visible.

You should own this now. I am not sure how much remains to be done here. Generally we have solved the label readability problem by making the background opaque, which you may have already done in the process of making it possible to annotate this graph with more complete peptide fragmentation information.