GC, GC-MS, Troubleshooting, Thermo Scientific

There are many problems that can get you into trouble when using a GC and GC-MS. For me the most time consuming, costly, and frustrating is the leak. These things cause no end of problems in your GC-MS system. They will lower the sensitivity of the method, cause you to lose a lot of carrier gas, could damage your column, and damage the mass spectrometer source. You can get lucky and find them right away or they can take days to track down (the second is usually my luck). Many of these will be obvious but when you are the most upset they seem to be forgotten, unless that is only me but I’m guessing it’s not. GC GC-MS leak checking can be a little more difficult than on an LC. With an LC when there is a leak you get a puddle, there isn’t much puddling of carrier gas on a GC. Sometimes a leak on a GC-MS can be seen in the MS tune page, look for masses 18, 28, 32, 44 and their relative intensities.

Like what you are learning?

Sign up to stay connected with all Thermo Scientific resources, applications, blog posts and promotions.
Keep Me Informed!
  1. Thoroughly check your connections. If you have recently made any gas connections to the GC check there first. Here is one of the obvious ones but also can be easily forgotten. Also, may not have been written in the lab notebook if someone was working on the system just before you (this is the one that I would always blame, even if it was only me using it).
  2. Make sure the septum is seated well and if it is old replace it. Reports on the number of times septa should be replaced will vary. I suggest just keeping an eye on it; they will eventually develop holes and will leak. Personally, I replace them daily with heavy use. The needle will make a big difference here. Careful with a bevel tip needle. They can develop burrs and core the septa, look for other thoughts on this too.
  3. Checking the bottom of the injector. There are metal on metal points at the bottom of many injectors. Make sure these are tightened well (please don’t strip the nuts). The column ferrule needs to be well seated, meaning not easily moved. It does not need to be tightened with a large wrench; we certainly do not want to crush the column.
  4. Column connections. If you are one of those that likes to connect columns together with press fit connections I applaud you. It usually takes me three times to get a connection like that to be leak free. Cut the column flat and straight, take your time. Give it a little pull to make sure it will stay together (very small pull, we don’t want a good connection coming apart).
  5. Connection to the detector. Seat the column with the ferrule so that the column does not move. Do not over tighten here, you can leak carrier gas out and air in to the MS. If you hear a metal on metal squeaking sound you might have gone too far.
  6. Look to o-rings around the manifold if you had the manifold open for some reason. I have used laboratory wipes and a very small amount of water to wipe the o-rings. This just makes sure there is no particle causing a gap and leak.

One last thought, if helium is your carrier gas use a helium “sniffer” detector. They can really be useful. Ok, this is the last thought; use a can of high purity electronic duster for a MS system. Spray a little and look for ions 69 and 83, for the brand we use. Just spray a little directly at a connection and wait; then move to the next connection. If you spray too much you see the masses and know they have a leak but not where. Please do not use Snoop, it contaminates everything.

Remember, leaks are frustrating but if you keep your calm and work methodically they can be found and fixed.