GC-MS, ISQ, ITQ, TSQ Quantum XLS, Trace 1310 GC, Thermo Scientific, troubleshooting

You are running samples and it appears that your GC-MS has contamination. You do a library search on the spectra. It comes back siloxanes. Where do they come from? How do I get rid of them? Are they affecting my analysis?

Yes, they affect your analysis. They will coat the MS source forcing you to clean, maybe even before you are ready to. Now, where do they come from? You might jump to the conclusion that it is the column and it should be replaced. Did you think injector septum or septum on the sample vials? How would you know the difference? We could get technical and get very specific but my rule of thumb is rise in baseline is the column; peaks at regular time intervals are from septa.

The Column

There has been a lot of work to show what column baseline and that rise looks like. I do not pretend to understand the chemistries that are involved, they are cool and impressive (I really do like chemistry). I would love for my Thermo Fisher Scientific colleagues or those from SGE and Restek to jump in here (anyone else could join in too). I have damaged columns from too much heat and from samples. Careful what you inject and know that the columns will not last forever. Remember, there will come a day when you will have that one sample that will completely take out a column, regardless of manufacturer. Everyone does that at one point, I’ve done that more times than I care to count.

Injector Septa

If you are using a split/splitless injector the septum could be at high temperatures for a long time. They also get continually punctured. In a previous post I stated to replace them regularly. No reason to go more than 50 injections, if you can help it. There are many different types of septa, I choose based on temperature of use. Those that are rated for lower temperatures make a good easy seal at those temperatures but will get that greasy feel if left too long at high temperatures. That will provide the regular siloxane peaks, probably through some complicated chemical process. The septa rated for higher temperatures provide that good seal when hot but can be hard when relatively cold. At the cooler temperatures they may easily core or even bend needles. It may not be so obvious but your syringe needle can have an effect here. A beveled tip can form a burr. This burr will eventually core the septum and push pieces into the injector. These will out gas, also causing those regular peaks. Personally I prefer a conical tip needle but they have drawbacks too, nothing is perfect.

Vial Septa

One thing to keep in mind, puncture only once. After that you will see that the sample gets contaminated by the material; that is unless they are held cold (and even then it will only be delayed). Solvents used in GC analysis have a tendency to be somewhat volatile, which is why we use them. The good news is they work well with GC. The bad news is they can continually extract the material of the vial septa. If after the first injection of a vial you don’t get evaporation you will see some extra peaks from the vial septa. The longer it sits the more and greater intensity peaks you will see.

There is no way around it, when you analyze samples on a GC-MS you will see siloxanes. The trick is to recognize where they come from and correct the problems. There are a lot of resources available to you, from SeparatedByExperience and other companies, to help with this and many other problems. I would love to hear from you on problems like this and how you fixed them.