Column contamination without access to column

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

4 posts Page 1 of 1
Hello,

we are currently working on a Agilent 5973N GC-MS, and has for a couple of weeks been dealing with excess amounts of background noice. We have put a block on the interface to the MS to verify that the background is not coming from the columns. When running a standard injection, the noice is still the same. We also get a temperature dependence on the MS, something we have never seen before when connected to the columns. The peaks in the noice are found at almost all au's. The most dominant peaks are at 207 and 281, strongly indicating polysiloxane contaminats from the column or elsewhere (we are running with a Gerstel Septumless Head Inlet) - which is strange, since no column material is attached to the MS-chamber in this case.

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We have cleaned the Ion source twice with no results, the turbo-pump line looks clean, the ion chamber itself has been thoroughly examined, the ion chamber is well-sealed (10%> abundance of N2-peak relative to the 69-peak of PFTBA). The only option we can imagine is that some column material is stuck in the interface, but since the interface is at a constant temperature we cannot see the temperature dependence of this explanation.

We wonder if anybody has encountered a problem like this before, and what the solution might be.

Sorry for the long read, and we wish you a pleasant day.
You don't have any stray bits of column in the MS by any chance?
Hi

It is an interesting problem, typically with the column removed and a blanking plug installed the baseline should be quite clean. You may see some low mass noise, but siloxane (207) should not be a significant abundance after cleaning and capped off.

I agree that maybe there is some broken column in the transfer line. One thing that would be interesting to try:

Configure an MS only instrument in the software. Launch the instrument and create a method that has a 0 minute solvent delay, 10 minute run time, scan 50-350 m/z N=2 speed.

Use the GC keypad to turn the oven temperature down to 35 C, and also turn the MS transfer line down to 35 C. Collect one blank run with your oven and transfer line cool, no column installed and with a blank nut/ferrule installed. Source and quad should be at normal operational temps (230 C, 150 C)


Next, do a second run but this time during the 10 or 20 min MS run, gradually raise the temperature of the transfer line in say 20 or 50 C increments. Do you see a clean baseline with it cool, and a bad baseline with it hot? It sounds like you may have already tried this, but independently changing the GC transfer line temp w/ an MS only instrument.. maybe not.


If you do suspect the transfer line is contaminated or damaged I recommend having a service person take care of it. It is not terribly difficult, but you need to be careful replacing it as the screws that mount the transfer line to the MS are in the chassis itself, so if you were to crossthread these screws you'd be in a serious pickle! Also there is an o-ring here that needs to be seated right or you will have leaks.

Anyway,... the transfer line could be contaminated. If you've cleaned the source it is unlikely for siloxanes to be there. Final thing: you mention you see peaks at "nearly every mass." Is it TRULY that you see like 20 or 30% abundance at every mass, with some ions showing above this level? If you have detector noise you will see "mass independent" noise like this. I've seen it where I could still see the PFTBA calibrant normally, but I had a mass response of ~20,000 counts at every single mass 1-1050 m/z. In this case I needed to blow some dust off the detector. Recommend having a service person consider this if they come out to change the transfer line.
Thank you for your suggestions - we eventually solved the problem by cleaning the transfer line even more (also with a piece of steelwire, which isn't optimal) and cleaning the MS source once more with isopropanol, CH2Cl2 and ethanol.

Thanks again!
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