Siloxane peaks from Atomx purge and trap!

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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We are seeing two discrete siloxane peaks after routine maintenance on our GCMS. Peaks have ions 207 and 281. These peaks are interfering with our compounds of interest and we are looking for help to troubleshoot this issue.

Routine Maintenance steps:
1. Cleaned the Ion source, changed the inlet liner, and septum.
2. Changed the analytical and condensation trap in the Atomx Purge and trap. Also changed the sparge glassware and internal standards on the Atomx.

The MSD tuned went well and we started out by running a water blank and started seeing the two discrete peaks around the time of our internal standards.

We assumed it was the inlet liner or septum so we changed out the liner and septum. We continued to see this problem so we began thinking it was the column- exposure to oxygen perhaps. So we changed the column and gold seal. When the new column was installed, the tech was unaware that the new column should not be connected to the MSD while conditioning. So we cleaned the ion source again and disconnected the column and baked for 4 hours with 2ml/min flow and then baked out the MSD.

Again, we ran a water blank sample and the discrete peaks were still there. So we decided to isolate the issue and started with manual tune scan on the MSD. The MSD did not pick up any 207 ions. So next, we ran the GC only- no injection and we didn't see the peaks. Next, we ran methanol direct injection on the GC and did not see the siloxane peaks.

So we went back to our purge and trap. We changed the analytical trap and condensation trap again and baked them out at recommended temperatures. Peaks still there. We skipped through the purge right desorb stage and the peaks are present. We ran an empty vial and the peaks are there. We ran no internal standards and the peaks still remain. We are quite stumped at what to do next. Does anyone have experience with siloxanes coming from the purge and trap system and where to isolate?

The Atomx purge and trap is connected to the GC via transfer line which shouldn't have siloxanes.

Here is some of our instrument info:

5973 MSD Hewlett Packard
6890 Agilent GC
Column: 1st column was DB-624 Agilent 60m x 250um x 1.40um
2nd column was Rxt-624 Restek 60m x 250um x 1.40um
Pressure: 16.1, Flow: 1, Carrier gas: Helium, Constant flow

Inlet: Split
Temperature: 250, Pressure: 16.1, Split ratio 40:1, Split flow: 39.7, Total flow: 43.2, Gas saver off

Initial 35 for 5 mins
Ramp 1: 104
Ramp 2: 142
Ramp 3: 230
for total of 30 mins

Internal standards used in Atomx: d4-dichloroethane, tolene-d8, and bromoflurobenzene.

Peak ions showing cyclotrisiloxane and cyclotetrasiloxane.

Any help is greatly appreciated!! We are out of ideas!!
Siloxanes are used in many creams and pastes. Polydimethylsiloxane (PDMS) has many degrees of polymerization and have molecular weights running from 300 daltons (a liquid) to millions (which is a solid). Dow is the main manufacturer (they have competitors) and PDMS can be found EVERYWHERE!
I would check the seal on the purge and trap, in particular the cream used to seal the joints!
Thanks for the reply- what seal on the P&T are you referring to?
Don't over look the septa. I found lots of phthalates in the "green" septa that were interfering with my 525 method. I now use Agilent red ones.
Bigbear wrote:
Don't over look the septa. I found lots of phthalates in the "green" septa that were interfering with my 525 method. I now use Agilent red ones.

Would you not see the siloxane peaks in the GC only run if it was the septa? We use the red Agilent ones as well.
If the peaks show up from the Atomix then look for where the contamination could be. I had two constant peaks from my new Atomix that took 6 months to completely disappear. They eluted near naphthalene so they weren't a problem and I ignored them.
I have had problems on my OI Eclipse where a contaminant made it through the trap to the 6 port valve and was "injected" every time the valve moved. That was solved using a solvent flush while manually switching the valve. I haven't had to do that with the Atomix.
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