Mysterious missing ion in SIM method...where did it go?

[rosemaryandsage47]

For the last month I've been trying to troubleshoot an issue that appeared rather suddenly.

This is a quantitative method using SIM for a suite of compounds.

One of the ions corresponding to a compound in my SIM method has disappeared in my lowest calibrators and low conc. samples and the signal is almost halved for high concentration calibrators. I'm still technically able to detect it but with greatly reduced signal. The other ions are unaffected.

I cleaned the source and the autotune looks great for both filaments, no contamination, reasonable repeller voltages and gain factors.

This issue appeared after I switched to a new filament and tuned it. When I cleaned the source I replaced the filaments.

The source cleaning improved the chromatography and response of the internal standard but didn't solve my issue of the missing ion.
It's a halogenated compound that has the highest detection limit of the suite of compounds I analyze for. It's the only ion that is having this issue.

Right now I'm analyzing the lowest and highest concentration standard of this compound with two different tunes corresponding to two different filaments so we'll see what that looks like.

I suspect this is an ionization issue of this specific compound which is why it has always had such a high detection limit compared to the others. I remember my analytical chemistry professor telling me that certain halogenated compounds have a difficult time ionizing via EI.

[Arne]

Is it possible for you to share the identity of the halogenated compound? Or if not at least the class of compound and which halogen is present?

[cjm]

I would check the method threshold isn't set too high and also check that the ion you're searching for doesn't have significant mass defect. i forget which compound we had trouble with but changing the ion by 0.2 or 0.3 amu solved the problem.