GC/MS Leak (Intuvo 9000+5977B SQMSD)


I am having a problem with GC/MS system leaking (Intuvo 9000 with 5977B SQMSD).

Pretty much out of nowhere, a leak in GC side appeared. MS rules out, as it was enclosed - and leak is non appearing, both in AWL check and simply while profiling air masses. Most usually, with AWL check, there used to be about ~2-3% N2+O2 in system. Now the N2 is jumping ~15-25% and O2 to about 5-7% - nothing was changed prior to it. Leak can't be detected inside GC using air canister, neither with hexane - while profiling appropriate masses for both.

Using the GC "Leak and Restriction" test, system shows unstable (jumping), about 0.1ml flow rate towards restriction.

What has been changed so far:

  • Gas Filter (Big Universal Trap);
  • Septum;
  • Liner and its O-ring;
  • Guard Chip (split/splitless);
  • All compression bolts (except for guard chip);
  • Column and MS Line gaskets (polyimide, 350°C).

Appreciate all the suggestions and ideas, thank you!

  • Which ion source is installed? What is the column configuration and the flows? Do you have a splitter installed?  How long since you replaced the GasClean carrier gas filter element or is it only the Big Universal Trap?  Did it start after changing the tank?  Have you used a gas leak detector on all fittings and valves prior to the GC?  Is this the only GCMS on the tank?  Have you done a leak-down test of the carrier gas supply?

    The N2:O2 is about 4:1, so air is the best suspect, for sure. If you have the extractor ion source installed, try changing the flow down to 0.6 ml/min and see if the air goes up or down and raise the column flow to 1.5 ml/min and see as well.  This is not a super valid test as the change in column flow changes the sensitivity of the system and the way PFTBA enters the ion source, but it often tells something.  If you have the HES ion source installed this test is not valid as the changes in response with flow also change the spectral tilt so at higher column flows the air always looks higher.

  • Hi!

    Sorry, that I didn't provide enough information.

    • Ion source installed is "Stainless Steel (SST) EI 350";
    • Quad Temp: 150°C;
    • Source Temp: 230°C;
    • MSD Transfer Temp: 250°C;

    • Column installed is DB_WAX_UI (123-7033UI)  30m x 320μm x 0,5μm   -  flow rate: 4 ml/min  -   with oven program:
      • 120°C - hold 5 min;
      • 8°C/min up to 230°C;
      • Hold 8 min;
        • Total run time: 26,75 min.
    • No splitter installed;
    • Septum Purge: 3 ml/min;
    • Split Ratio: 1:50
    • Gas Saver: 15 ml/min - after 3 min.

    As a filter for helium gas, only Big Universal Trap is used, without GasClean filter. And no, leak didn't start after changing the filter, it started prior to that (it was only changed as a precautionary). Nitrogen inside new filter was purged.

    Have you used a gas leak detector on all fittings and valves prior to the GC?  Is this the only GCMS on the tank?  Have you done a leak-down test of the carrier gas supply?

    Yes, all fittings and valves were checked for leaks prior to the GC. No leaks have been found. Yes, it is the only GCMS on the helium tank. And yes, carrier gas supply is all good.

    Even without extractor ion source, I did some AWL's with 0.6ml/min, 1.5ml/min and 4ml/min flow rates.

    0.6ml/min  Flow Rate:

    1.5ml/min  Flow Rate:

    4ml/min  Flow Rate (method's flow rate):

    What I don't clearly understand - shouldn't abundance of N2, O2 etc. ions be higher with 4ml/min flow rate - compared to 0.6ml/min and 1.5ml/min flow rates? As prior two have much higher abundances of these ions.

  • Only now I stumbled upon such tip. I will make corrections in the method and do comparative analysis.

    Thank you once more!

  • I suggest you change to a narrower bore column, 121-7022-INT  J&W DB-WAX Intuvo GC column module, 20 m, 0.18 mm, 0.18 µm. (compatible only with the Intuvo 9000 GC System)  and run that at 1.0  ml/min.

    One other important bit.  15 ml/min of GasSaver flow may be insufficient.  Yes it's an allowed setpoint, but I have seen air in the MS just from not enough total GC inlet flow, especially at higher oven temperatures.  Consider changing that to 30 ml/min.

  • Thank you for the suggestion regarding the GasSaver flow. Are there any recommended intervals for that function - or that depends solely on total flow of the inlet? It seemed a bit for a smaller side (as in 15ml/min) but didn't know if that would be enough or not.

    About the column. Are there any other points why you would you recommend using narrower column instead of 0.32mm one? Or is it solely because of higher sensitivity for MS using lower column flow rate?


  • There are a few ways to use GasSaver. If you're using the inlet in Split mode, the GasSaver should be turned on as soon as you know for sure that all of the sample has exited the inlet and is on the column. Two minutes is typical, but it could be shorter, especially if running very high split flows.  If using the inlet in Splitless or Pulsed Splitless mode or ramping the temperature of an MMI inlet, the GasSaver time must be longer. Too low a GasSaver flow fakes operators into thinking there is an air leak. 

    Or, set the Gas Saver time to after the run is already complete.  Then Gas Saver will be ON when the GC is not running but OFF during the run, ensuring that the flows are sufficient.    If you need to save even more helium, consider purchasing a Helium Gas Saver module for your GC so that nitrogen is used all of the time that the instrument is not running samples.

    The smallest volume injected of the lowest concentration of the cleanest sample possible results in the least amount of inlet, column, and MS maintenance.  A narrower bore column has lower loading capacity and makes sharper peaks. The smallest peak of interest only needs to be 3x to 5x taller than the average background baseline.  Too many have huge peaks and then wonder at the associated maintenance.

  • Very informative insights about the GasSaver! Concerning my peaks of interest - they are highly symmetrical and not overloaded, but I guess I could push it into the lower side, so the sensitivity would be higher.

    If I would have any technical questions in the future, could I contact you? Thank you very much!

  • Post questions on the community. I'm one of the folks answering. You can also call the toll-free number in your country and talk to someone on the phone.

    and you are welcome!

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