Chromatography Forum

Hi All,

I'm running an Agilent 6890GC/5975MSD system and having a problem with the baseline dropping below zero. It starts out fine, then dips below zero around 5min, eventually rising above during the end temp ramp. It does not happen on every run, but it is becoming more frequent. I have seen this problem on two different systems running different analyses with different columns. I am running cnst flow on both instruments, but different temp programs. Increasing/decreasing column flow has no effect. I have replaced one ion source assembly with an entirely new one, replaced the inlet liner, gold seal, reinstalled the column, etc to no avail. Autotunes on both systems check out and do not indicate any leaks. Has anyone else encountered this?

I'd appreciate any help/ideas.

Is it dipping to zero, or going below zero?

If your threshold count is set high, then perhaps you're not having enough ions in the quads to trigger the TIC. Try setting it to 25 or 50 (default is 150 for Chemstation 1701CA).

The base line is actually going below zero. My threshold is currently set at 100. I'm setting up to rerun using a lower threshold as you suggested. I'll keep you updated!

Thanks!

Lowering the threshold to 20 finally brought the baseline back above zero.

Thanks for the help!

Good work.

I assume that you are in SIM mode, and collecting only a few ions at high masses?

Actually, I'm running in Scan mode.

I had the same problem with mine. Changing the threshold fixed it as well. Never found out why the original threshold was no longer suitable.

Not sure why this started either. It occured on two different GC/MS systems for two different analyses. The only common element was the column phase. The previous analyst (running a different analysis on a different column) did not have this problem. I'll be changing column type next week for another similar analysis, so it'll be interesting to see if I notice any difference. Thankfully, I haven't had a problem since I lowered the threshold.

There was a small air leak in mine, but as we were in a rush to get the instrument back up and running we didn't have time to check to see if the threshold came back up after the leak was fixed. I wonder if your carrier supply has some air in it as it is affecting two instruments?