Typically, the mass accuracy of fragments vary between 0.01 - 0.05 Da when they are analysed in Orbitrap. Some devices allow to scan fragments in linear trap where mass accuracy became ~0.3 Da

Mark, thanks

I think most of the MSMS fragments are charged but i dont see isotopes. i guess your not suppose to in ms/ms, that's the only way the masses calculate out. I'm concerned if i optimize the collision energy I will fragment too much and miss the low end. i guess I could do MSn in the trap. Is this how you would proceed? New at this.