High level of background noise in GCMS can be because of many factors. The columns also can be culprits. But if they are OK, then you will have to look at other possibilities. Do a MS tuning and look at the detector voltage. If it is on the higher side it means the detector has aged and may be it requires a replacement if all other things are OK. A high detector gain will definitely increase the background noise level.

Hi Amy,

What masses contribute to the high background?

Regards, Alex

Hi Amy!

If I would suspect column and would like to exclude it as nose source I will remove column  from MS inlet and use nut with no hole ferules (or no hole universal nut) to block MS inlet (as usually it supplied with new instruments). Pump down instrument and try to read the noise. In this case you will definitely know is it column and GC or MS source of noise.

Andriy

Thanks for the advice. The masses that contribute to noise are 44, 57, 91, 207, 281. These are the major ions, but there are many other masses in between these. It's a messy spectrum. I know that 207 and 281 are septum/column bleed more than likely, but I put on a new column and replaced the septum and still had these values popping up. The gain appears to be in the normal range. The only column I haven't changed recently would be the inert column into the mass spec. 

On another point of terminology; the connection between the CFT and the MS is not a column, it is a transfer line. It has no stationary phase in it, and it does not contribute any chromatographic separation.

Lots of details here that are missing. What was your background previously? What kind of liner did you install (these are pretty typical ions for liner bleed)? Do you have flow through the back column? 

One of the issues with the CFT is that it is typically at oven temperatures, not transfer line temperatures. Do you see the bleed if you set the oven to your transfer line temperature? Also, changing filaments requires that you re-tune your MS; did you do this? A sagging filament, which sounds like what you had on the first filament, will give you significantly lower background than a new filament. 

Since you clearly did not have the problem prior to cleaning I wouldn't suspect the transfer line, but without additional information it is hard to help.

Hi Amy

In addition to the moisture trap you need a scrubber for organics and for oxygen. The most convenient gas scrubbers combine all three functions in one. I have had bad experiences with the kind that have plug in transparent plastic elements.

The transfer line column is inert fused silica, but I was running it at lower temperature because I quantify thermally liable compounds. I was concerned of possible active sites in the transfer line due to the lower temps. I always re-tune after I've cleaned a source, and my tune values looked normal. I have not yet isolated the mass-spec. The scrubber for organics is a good idea, and I will look into it. Thanks for the advice!

Hi Amy

Since the transfer line (NB it is not a column, it is an inert tube) has no stationary phase in it and no retention, and is under vacuum you may be safe to run it at a lower temperature (lower than what ?) but if your aim is to avoid thermal degradation then there is no point in having it cooler than the temperature at which your thermally labile analyte(s) elute from the column. 

Over time the transfer line will gain a coating of stationary phase and other muck that has bled off the (real) columns. It will then start to retain analytes (which you do not want it to do) and bleed the contaminants into the MS.

The transfer line temperature is not lower than the temperature the compounds elute off the column. The lower temperature is also to avoid hydrogen abstraction of the compounds in the transfer line.   I'm thinking that's probably what is happening at this point, and I've run some pretty nasty stuff. I think it's time I replaced the transfer line. I suppose I'm dragging my feet on this one. Venting now...

http://pubs.acs.org/doi/abs/10.1021/es0205582