We see this phenomenon often enough in our analyses (mostly drugs) that we routinely look at effect of isolation width on fragment spectra signal when analyzing a new compound. Aminoglycosides, some macrolides, and others seem to do much better with an IsoW of 4.0 rather than 1.8. I've heard them called "fragile ions"--something about the trapping conditions causes them to fragment prematurely. If any one knows more details, or how to predict you're going to have a fragile ion based on structure, I'd like to hear it.

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