Prepare GC/MS For Column Maintenance

Hello Everyone,

I'm very new and don't have much experience in troubleshooting the GC-MS so I need your help. I'm operating on Agilent 7890B and 5977 MSD. Recently I've noticed very big baseline noise. I have changed the inlet septum and liner, which helped a little bit, but not enough. I suspect that contamination might be already in the column so I would like to trim the column and bake it out. Could you please let me know how should I prepare the GC and MSD for this process? I know that I have to cool the oven and inlet to room temperature, but what about the MSD and gas flow? Should I vent the MSD (the column is connected directly to MSD), and what about the carrier gas (He), should I close the cylinder?

If someone would be able to help, I will appreciate this a lot.

Thank you.

  • Hello, I understand you disconnect only the injector side of the column in order to trim it. Just be careful not to break the column closer to the transfer line because the sudden high flow can damage the pump and the oxygen entering can oxidize the hot parts of the MSD. It happened to me once...

    Indeed, venting the system is annoying due to the time lost in cooling/heating the hot parts, slowing down the pump, recovering vacuum, air and water entering the system and possible leaks appearing.

    I don't like to loose vacuum so I created a maintenance.M file where the hot parts of the MSD are at 100ºC in order to avoid oxidation when oxygen might get in the column (column must be cool or it will be damaged by oxygen). When I need to completely remove the column, I vent the system until the pump is at 40% speed, disconnect the column, plug the transfer line and pump down. The problems mentioned above are reduced and, especially, no leaks will appear.

  • If u can share picture of columns connection in oven then i can say something...

  • There is more chance of problems with high flow to a Diffusion pump, as the faliure is called a backstream - diffusion pump fluid vapor throughout the system, an incredibly expensive repair.  On diffusion pumped systems it is safest to set the system to VENT and let the diffusion pump get cold, about ten minutes, before cutting the head of the column.   

    Make sure and cut enough off, like 30 to 50 cm.

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