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GC GC-MS Troubleshooting Part II; Siloxane Peak Contamination


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.


You mentioned that the siloxanes will coat the MS source forcing you to clean. Could you please elaborate a little more. When I block the entrance nut everything is good. But when I run using methanol I see the regular siloxane peaks. You meant the regular siloxane can coat the MS surface and tend to give rise siloxane peaks later or noise ?
Posted @ Monday, March 26, 2012 8:15 PM by hooshang pakdel
When these compounds coat the source your intensities and sensitivity will decrease. To be able to continue your analysis you will need to clean the source. 
If you are seeing peaks of siloxanes when you inject solvent then the siloxanes are either in the solvent, the injector, or the beginning of the column. I would suggest injector maintenance. Replace all consumable parts, sonicate all metal parts that can be removed, and rinse the inside of the injector with solvent.
Posted @ Tuesday, March 27, 2012 6:54 AM by Eric Phillips
Agree with Eric, and if siloxane are appearing only with MeOH, then solvent contamination could be the first reason and residues washing from inlet liner could be the another reason.
Posted @ Wednesday, June 27, 2012 12:34 AM by Pravin Mutiyar
What would you suggest if I am still getting siloxane peaks after having replaced the septum (to a high temp one) sonicated all parts that I can remove, replaced the liner, cleaned the source, baked the column and removed 20 cm... I get a constant 207 m/z without even injecting which suggests to me its the inlet, the column or the source.... very confused!
Posted @ Wednesday, February 19, 2014 4:30 AM by Holly
Hi Holly, 
Thank you for your questions. I have forwarded to our GC experts and they should respond shortly. 
best regards 
Posted @ Wednesday, February 19, 2014 6:48 AM by Sonya Pelia
Hi Holly, 
As per our expert, do consider doing the following: 
1. Isolate the mass spectrometer by capping off transferline. 
2. If you still see 207, then remove the source and look for piece of broken column inside the source. 
Hope this fixes it. Let us know if you have further problems. 
Best regards 
Posted @ Friday, February 21, 2014 11:22 AM by Sonya Pelia
Headspace SPME (fiber=PDMS) GC/MS for VOCs. Seeing massive amount of 149, 177 and 223 ions every run. Replaced every consumable, trimmed 20cm, baked out injector, baked out column, baked out ion trap. First run after bakeout looked ok (just ok - still low level ions in the baseline), second run horrible again. Chromatography looks good until contaminant comes off and spikes well over 1M cts. 
Direct inj with isopropanol still show contamination. Have changed fibers, vials, vial septa to no avail. I am down to thinking severe injector contamination. Any other ideas?
Posted @ Friday, June 20, 2014 3:46 PM by AG
Hi Angrasham, 
My apologies. This comment slipped my vigilance and I just saw it. I have forwarded it to our experts and hope to have an answer shortly. 
best regards 
Posted @ Thursday, August 21, 2014 11:17 AM by Sonya Pelia
Hi Angrasham, 
From what you describe, it sounds like it is likely coming from the injector, unless you are also using the same isopropanol in your headspace vials and that's the source of the contaminant. If you are using isoproanol with your headspace injections you could try direct injecting a different solvent, or just running the method without injecting, to check to see if your solvent is contaminated.  
Best regards, 
Posted @ Thursday, August 21, 2014 2:39 PM by Jason Cole
Hello all, 
I am having the same issue with siloxanes in both 5973/6890 instruments and I depleted all my resources. I started seen the following compounds tetradecamethyl cycloheptasiloxane, decamethyl cyclopentasiloxane, and dodecamethyl cyclohexasiloxane in every injection in only one instrument because the other was out of service due to a bad computer board. But when I got the out of service instrument working i noticed that it had the same contamination. I had replaced the liner, o-ring, septa, gold seal, column, syringe, wash vial, split line, and the shell weldment. I am not sure what else could it be. I have also try an air injection, an injection without solvent, and I am still seeing the three peaks of siloxanes. I haven't touch the mass spect so far and not sure what else to do, help please. 
Thank you.
Posted @ Friday, December 19, 2014 10:40 AM by Saul
Hi Saul, 
If you had replaced the liner, o-ring, septa, gold seal, column, syringe, wash vial, split line, and the shell weldment; and still you are getting siloxane, there could be some other source for these contaminants. Can you elaborate what you are trying to analyse? Sometimes the extraction method also causes siloxane source. 
Look for solvent contamination as well. 
Posted @ Monday, January 12, 2015 10:28 PM by Pravin Mutiyar
Hi Saul, 
This just came in from one of our GC experts: 
In these trouble shooting situations, it is essential to take a step wise approach to determining the location of the contamination. I try to isolate each area of the instrumentation.  
e.g.)Autosampler, pre inlet, inlet, column, mass spec 
Then isolate each variable or part that could introduce potential contamination then replace each part and test.  
e.g.) autosampler  
Syringe, wash vials, wash vial septa, sample septa 
Remember to keep a log of the steps you have taken to help rule out other possibilities.  
It seems like you have been taking a similar approach.  
From the point that you are currently at, I would start with the mass spec. Vent the system and remove the column. Cap the transfer line turn the system back on and let it pump back down. Then I would then monitor the background for the ions in your siloxane peaks. If they are present remove the source clean and put it back in and retest.  
If not, clip both the head and tail of the column and re-install the column. Run another air injection. (no sample introduced, no autosampler or needle used).  
If the contamination appears in your air sample we have narrowed it down to the GC or the column and not your autosampler.  
Ask yourself the following questions 
How old is your column? Columns leach and breakdown over time. Is it time to replace it?  
Could any of the inlet replacement components have been contaminated after you replaced them? 
Are you using Snoop or another liquid to check your column connections? If you are STOP immediately. This can introduce the liquid substance to your sample path.  
Evaluate each section with quick tests to try and isolate the problem.  
Please keep in contact and let us know if the issue was resolved. 
Posted @ Tuesday, January 13, 2015 3:24 PM by Sonya Pelia
Thank you all for your assistance. But it turns out that the contamination was coming from a gas valve. My supervisor had recently added a gas valve on the backside of the instruments and forgot to let us know before leaving for vacation. I did not notice the new valve until later on. I did not know if that was the cause of the contamination but I had to try it. So I removed the valve and ran some samples and "voila" contamination was gone. But I do appreciate all the feedback that I got.
Posted @ Tuesday, January 13, 2015 3:59 PM by Saul
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