Chromatography Forum

Dear all,
I am working on a method that look for small molecule. Range of m/z from 100 to 600. I am working ddMS2 in confirmation mode but i am not able to obtain fragmentation values for each of the analyte concentration i am working with. The problem is that the parent compound is displayed in the FullMS spectrum but the ion that is detected deos not fragment. I have been playing with the Minimun intensity threshold value and the Maximum Injection time one as well, with no positive outcome. Anyone have some suggestions? Thanks

With very little information you provide I will take a few leaps of assumptions..

You are on an Orbitrap of some sort, most likely a QExactive.

If you get good MS spectra but poor or no msms spectra most likely your quad is dirty, not calibrated or maybe there is a hardware issue.