We are currently working on a school project and came across data on isoquercetin and quercetin.
When analyzing isoquercetin using a collision energy of 40, we observed only a single fragment at 303 m/z. In contrast, applying a lower collision energy to quercetin resulted in a greater variety of fragments.
Isoquercetin and quercetin are not the same compounds (isoquercetin is a 3-O-glucoside of quercetin). Therefore, they might produce different numbers of fragments at different collision energies.
What is likely happening in your case is that isoquercetin fragments to quercetin and glucose at the CE of 40 eV. Glucose is likely leaving as a neutral molecule which is why you do not see the corresponding peak in the MS, while m/z of 303 is most likely quercetin.
On the other hand, quercetin is an aglycone. As such, it has no glycoside bond that could be cleaved. This means that all of the collision energy will be used for the fragmentation of quercetin itself. This is why you see more fragments even on relatively lower CE.
If you increased the collision energy in the analysis of isoquercetin above 40 eV, you would most likely start to see some of the same fragments you see in the analysis of quercetin.
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