Chromatography Forum

Hi everyone,

We are having a problem with our 5972 mass spec. The instrument runs fine, and the chromatography is good, but we have a contaminant in our system with m/z=58. It comes out right from the start of the run till the end. We are pretty confident that this contaminant is coming from the MS because we see it in the MS even when the GC is disconnected from the MS. We have cleaned the source several times but the m/z=58 contamination has not gone away.

The abundance of the m/z=58 ion relative to the 69 ion is about 0.1 to 0.2, so it doesn't look that bad, but when we analyze samples of low concentrations, the abundance of the m/z=58 ion is usually greater than the other ions. This leads to mis-identification of those compounds that exist in small concentrations using the NIST library.

Is any of you familiar with such a problem, and if so, could you please give us hints on what we need to do in order to solve this problem?

Thanks in advance,
John

In a full scan are there any other ions associated with 58 - perhaps with the GC column removed from the mass spec?

We also see an ion with m/z = 43. But we don't see ions bigger than the 58 ion.

m/z 43 & 58 suggest acetone.

What do you use to clean your source ??

It does suggest acetone, and we did clean our source using acetone, DCM, and hexane about 5 months ago. Acetone being volatile, we would expect it to stay in the MS for such a long time, unless there is a cold spot in the system.

I meant we wouldn't expect acetone to stay for a very long time.

I meant we wouldn't expect acetone to stay for a very long time.

Could acetone possibly have become trapped/saturated into the diffusion pump oil and you are seeing some out-gassing from that?

If you cleaned the vespel or ceramic parts of the source with acetone they can out-gas for quite some time since the source in a 5972 isn't directly heated. The interface heats the source in that model and the farther you are from the interface the cooler the source is.

Does your instrument have the large or small ion gauge tube? If it is the large one, you may need to degas the filament as there can be some contaminates that collect on the cold glass of the gauge tube.

We replaced the diffusion pump fluid but that didn't help. We also replaced the repeller assembly because it had a ceramic part on it but that also didn't solve the problem.

Our instrument has the large ion gauge tube. How do you degas the filament in the ion gauge tube? I have never done that before.

Thanks for your idea.

I've seen acetone linger in the GC inlet and liner for a while after cleaning it out but it was usually gone within a few hours to a day at most. Could it be drawn into the system from the ambiet lab air or from the syringe rinse?

We also don't know why acetone would stay for such a long time in the system. I don't think it is coming from the ambient lab air because it is only happening to one of the two instruments we have in the lab. Given that we started to see the acetone contamination right after cleaning the source might suggest that it came from the cleaning. But then, staying for months is quite unbelievable.

Do you think it might be somewhere in the quad?

We replaced the diffusion pump fluid but that didn't help. We also replaced the repeller assembly because it had a ceramic part on it but that also didn't solve the problem.

Our instrument has the large ion gauge tube. How do you degas the filament in the ion gauge tube? I have never done that before.

Thanks for your idea.

On the controller for the large ion gauge there should be a degas button/rocker switch right below the display. Before it will activate you must be below 5*10^-5 torr on the gauge. If you are scanning when you activate the degas function you will see a spike of air, water, and other background masses, then see them slowly fall away. You don't want to leave it in degas mode for more than about 10 minutes or you can possibly cause damage to the filaments though I never had any problems with that.

Sorry I misinformed you. We actually have the small ion gauge tube because the controller does not have a degas button. I thought that it was the large ion gauge tube, but after checking on the internet, ours is a small ion gauge tube. Is it possible to degas the small ion gauge tube too? If so, how is it done?

Sorry I misinformed you. We actually have the small ion gauge tube because the controller does not have a degas button. I thought that it was the large ion gauge tube, but after checking on the internet, ours is a small ion gauge tube. Is it possible to degas the small ion gauge tube too? If so, how is it done?

The small ones don't have the function and if you keep them turned on most of the time they really shouldn't need it. I guess one could become contaminated if left off most of the time, but I have never done that to know for certain.