Ghost Peak and Elevated Baseline

I am using GCMS 8890 with a 7010B TQ system. We ran a blank and we're seeing a ghost peak and a baseline that we're unsure about. Most of the baseline is m/z 44 except for the weird "peak" which can be seen in the image below. There was no injection (the column was blank). We baked the column and that didn't help. It is a new column, Restek-200ms. The 7010B/8890 has a 1 mL/min flow and the oven temperature ramps 35-250 deg. C (column max of 320 deg. C). Gas filter is clean and we're using Ultra High Purity Helium. The Autotune/air-water checks are totally normal. And no leaks are detected.  

  • It looks like your scan range started at 30?  44 is CO2, so that big thing could very well be an air peak.   That bump is about 1 minute wide and happens after 1.3 minutes or so.  Using the Pressure Flow Calculator built into MassHunter and a guess - a 30m x 250uM x .25 column at 35°C oven, 1 ml/min flow into vacuum has a holdup time of 1.38 minutes. 

    Does your method run splitless?  What are all of your inlet, column, and oven parameters from your method?  What Electron Multiplier setting are you running in this scan method?  This spectrum would appear to show 1.2 million counts of oxygen so there would be about 5 million counts of nitrogen that you aren't looking at.  If you have an EMV setting that results in a Calculated EMV (V) that is higher than your tune, it could make it look like there is an air leak now.

  • Hi Paul, thanks for your quick response. I've been troubleshooting along with  and can answer your questions.

    - Inlet: Splitless, Purge Flow to Split Vent 100 mL/min at 1 min; Gas Saver 20 mL/min at 3 min; Septum Purge Flow 5 mL/min; 250C

    - Column: 1 mL/min; Holdup time 1.3824 min. You were right about the dimensions. Oven: 35C for 6min, 6C/min ramp to 150C, 50 C/min ramp to 250C

    - Collision gasses: He Quench Gas 4 mL/min; N2 Collision Gas 1.25 mL/min

    - MS: Detector Setting Use Gain Factor; Gain 1; Calculated EMV 1680.1 (V). Autotune uses EMV 1379V, so you may be right about the EMV setting resulting in a higher Calculated EMV. I guess this is because we are using Gain Factor instead of Delta EMV? But with Gain of 1, should the Calculated EMV would be higher? Would this be sufficient to explain the 10x elevated baseline?

    I figured out that the huge peak is controlled by the Split Vent operation by varying the Purge Flow to Split Vent parameters (see screenshot below). From this, I think we can conclude that air is getting sucked in while the Split Vent is closed. Could the Split Vent Valve be faulty, even though it is passing the Split Vent Restriction Test? We used multiple methods to test for leaks around the inlet fittings while the GC was idle and didn't find any (digital leak detector, compressed air with tetrafloroethane), however it makes sense we didn't find any considering the leak (giant air peak) only appears when the method is being run.

    Red chromatogram (same as above):Purge Flow to Split Vent 100 mL/min at 1 min

    Green chromatogram: Purge Flow to Split Vent 0 mL/min (off)

    Orange chromatogram: Purge Flow to Split Vent 20 mL/min at 0 min


  • Hi,  !   and I have done some more troubleshooting and have a few updates. 

    We've changed a few things that are listed here.

    Inlet: Splitless, Purge Flow to Split Vent 50 mL/min at 0.5 min; Gas Saver 20 mL/min at 1 min; Septum Purge Flow 5 mL/min; 250C

    We are now using Delta EMV rather than Gain, and we are no longer subtracting the baseline. 

    We also noticed a few things for the Front Inlet during our blank injections.

    • During 0-0.5min (valve closed)
    • Setpoint:6.0 ml/min
    • Actual: 5.7 ml/min

    Black Chromatogram: The first run after the GC sat idle over night with the oven at 80C

    Red Chromatogram: All the same conditions, except that the GC hadn't sat idle at all before the run

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