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Hi,We have been having problems with our Agilent GC/MS in both NCI and EI, but only in SIM mode.We first noticed this after injecting a 1 pg standard, but now that we look back, we have been having this problem in SIM mode for quite some time. The baseline sits at 0 with random fluctuations, which look as if they are just electronic noise. We are still getting peaks. This is more of a problem in some SIM windows than others.
For example, a SIM window containing 6 ions (dwell time = 100 msec, so 1.6 cycles per second) looks terrible. Each SIM window is set up so that the cycles per second is more than 1.5.Agilent thought the problem was with our sensitivity, however increasing the EMVolts has no effect on the baseline. And since we have had this problem so long and the fullscan baseline looks fine, we have ruled out problems with our consumables. We are also experiencing the problem with 2 different columns and different instrumental methods.I have also been looking at some pine needle samples that have been run in SIM mode. These have a normal baseline, well at least a baseline that looks normal to my eyes. I'm continuing to look back at more of our runs from the last year.We have also compared our 1 pg standard to a similar 1 pg standard run on another GC/MS in SIM mode - the other GC/MS has a normal looking baseline.Any ideas??? I will try to work out how to post a chromatogram so I can show you guysThanksKaren.
The baseline looks bad compared to Simonich Lab because the scales in abundance are different:0-90 compared to 0-3000. There is nothing wrong with the baseline itself. The low sensitivity may be caused by problems in the front: split ratio too large? Low injector temperature?The cycles per second is a little low. For a peak with PW of 0.1 min, you only collect about 10 data points across the peak. It's recommended to have 15 data points for a peak. So shorten the dwell time to make it to 2.5 cycles per second.
JH1 - We are mostly concerned with the baseline and how the noise fluctuates.DonHilton - We are very regular with our inlet maintenance. I also changed the liner, septum and cleaned the inlet, and tried re-running with no luck (gold seal doesn't look too worn).
As we seem to have had this problem for a while and consumables have been changed a lot, we thought we could rule that out. The two instruments do have different columns (in length that is) and conditions.
I'm not completely sure about the liners, though I expect they would be using Agilent deactivated liners too. However, we have used a similar column and exactly the same instrumental method before and still had the problem then.Chemstation - Yes, the baseline for Simonich is ca 45, while ours is 0. These are both run in SIM mode - threshold is a fullscan parameter, although that was one of our first thoughts (it seems as if the bottom of the baseline has been chopped off?!).
We have run fullscan and SIM scan using the same method and still have the problem so don't think the method is corrupt. Also, we are having the same problem with different instrumental methods and different columns. The standard mixture is not exactly the same - they are both mixtures of organic contaminants (organochlorine pesticides, other pesticides, polychlorinated biphenyls) - the Simonich standard contains more analytes and slightly more variety of chemical classes than our standard (it was run a few years ago when my supervisor worked in the Simonich lab).JI2002 - We are running pulsed splitless injection with inlet temperature of 250 deg C and for some methods 270 deg C, depending on what we are looking for. I'm running the standard again with cycles per second no lower than 2.5 so will see how it affects the chromatogram. Dwell time and cycles per second seems to be one of those iffy things. Agilent recommended 6 scans across a peak, while someone else recommended no less than 1.5 cycles per second.I will try and post some more pictures of the baseline.