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Restarting your GC after its Christmas Holiday

11 Dec 2023

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If the laboratory is not staffed for the time between Christmas and New Year, it is a good idea to shut down devices, saving electricity and carrier gas.

However, without taking appropriate precautions, unpleasant surprises might await you when you start the GC again:

  • An unsettled baseline due to impurities in carrier gas lines or on the column.
  • Ghost peaks due to condensation of moisture and impurities dissolving in the system.
  • A rising baseline because of leaks can mean oxygen in the system. This can ultimately lead to bleeding if the column is heated up too quickly and damaged.

What happens during the shut-down? 

  • The injector septum made of silicone - the same material as your stationary phase in WCOT siloxane capillary columns - releases a certain amount of degradation products as usual at elevated temperatures, which reach the column via the carrier gas flow (a part of this is already directed to the outside through the "septum-purge" flow, but a noticeable amount still reaches the column).
  • As long as the column is cold, these degradation products collect at the head of the column. This accumulation increases over the shut-down period. When the first temperature program is started, these siloxane fragments elute.
  • It is not only degradation products from the septum, but also impurities from the injector and the carrier gas (sample components deposited there, septum crumbs etc.), which slowly evaporate and deposit on the cold column.
  • These two effects are amplified if the split valve is closed during shutdown or if the split flow is greatly reduced. Although this is sensible as a gas-saving measure, it increases contamination of the column from the carrier gas and injection system. A possible solution is an open split with a high split flow.

When using helium as a carrier gas, it diffuses out of the capillary when the GC is off and a slight negative pressure is created. Ambient air, containing impurities, is drawn into the GC. Moisture recondenses in the GC and dissolves impurities in the system. Its also possible that components from the split vent trap migrate back into the split line and cause problems.

You have the following options to fix this:

  • Shut down the GC
    • Cool the injector port, the GC oven and the detector to room temperature and turn off the gases. Then remove the column, closing it with column caps or septum pieces and store it in a box or cabinet.
  • Recommissioning:
    • Check or - if necessary - replace the liner and septum, reinstall the column, slowly increase the flow back to the usual flow rate and purge the system for 30 minutes at room temperature.
    • Adjust the fuel gas flow, increase the injector and detector temperature to the usual setting and switch on the make-up gas after ignition of the flame.
      • Successful ignition of the FID can be achieved by checking for water condensation on a cold beaker or watch glass.
    • Now start the following temperature program 40°C (10) at 10°C/min up to the Tmax of the column (30min) to remove impurities.
      • For examination we recommend to inject pure solvent (preferably suitable for your analysis or a suitable column test mix or the with which your column was originally tested) so that you are sure that all parameters are correct and your GC is ready for operation.

  • For a short standby for the weekend or a few days
    Carrier gas flow 0.5 - 1ml/min
    Reduction of the split flow to 5-10ml/min
    GC oven temperature 60-70°C
    Injector temperature 100°C
    Detector temperature 150°C
    Always keep the flame burning in the FID. 

  • For a long standby for several weeks
    Carrier gas flow 0.5 - 1ml/min
    Reduction of the split flow to 5-10ml/min
    GC oven temperature 40°C
    Switch off the injector, detector, fuel and make-up gases.

Installing a carrier gas cleaning system and checking for leaks beforehand using a leak detector provides additional safety.

There are certainly other tried and tested options. Which option you choose depends on how quickly you want the device to be ready for use again after the break (and on your laboratory budget!). We wish you every success and, above all, a smooth return to work after a well-deserved break.