Thank you for the answer.
> Under normal circumstances each spectrum will be associated with only one
> molecular system; there was only one sample and the molecular system
> generally reflects what's in the sample. So I would suggest checking the
> Mol Systems column of the main Experiments table and making sure that each
> experiment is associated with only the correct molecular system. If two
> molecular systems are selected then Analysis will think that both are
Yes, it seems that was the case - in the experiments table, some experiments appear to be associated with MS1 and MS2.
I might select wrong atom (of the wrong Mol System) when I assigned the peak, but I cannot find that one. Peak Table shows only chain, residue and atom of each assignment but not Mol Systems, and I cannot find the wrong one by looking at the experiments by eyes (some experiments are 2D and have only handful of assigned peaks so it should be fairly easy to look through).
Is there any way to find those peaks which have been assigned to wrong Mol System by mistake?
Also, I was probably careless enough to select the wrong one from the candidates in the assignment panel but it can happen sometimes. Is it possible to have 'warning' when unintended Mol Systems are picked during assignment?
> The molecular system setting for an experiment is added the first time you
> assign a peak to an atom within that system, so that it knows what to use
> in future. If there is a bogus molecular system association it is
> frequently due to a bogus assignment to an atom within that system.
I assigned the F1 and F2 dims as MS2 atoms and I still had candidates from MS1 and MS2 in the F3 dim table. I'm sorry if I misunderstand something but I'm still not sure why this actually happened.
Thanks for your help.