Peak is growing at 42.10 and creating autotune problems

Three million counts of anything inside the source is suppressing other ions and is a problem that should be resolved.  Even if you change your acquisition scan range the contaminant is still in the ion source, being ionized, and crashing on Q1.

How is the vacuum?  The turbo pump power reading?

Is it there all the time, in an MS1 Scan data file scanning 35-350 or so?

Are there other peaks besides 42.1?  What about with the PFTBA turned off? 

Is it a leak or a bad tank of gas? - Files - GC/MS - Agilent Community

I used MS Search to look for ion 42.1 and there are not many choices - Diazinine, Diazo-methane, Ketene, Cyanamide, Propene, Cyclopropane, and Carbonyl borane.... 

What happens to the peak when you turn the column flow down to 0.6 ml/min or up to 1.5 ml/min? Does the peak go down and up?  What about turning the collision cell quench helium to 0.00 ml/min?  Or turn the nitrogen collision cell gas down to 1.25 ml/min or up to 1.75 ml/min?  

What happens to the peak if you replace the column with another one?

In the tune what is the air/water check - or is it so overwhelmed that it can't do that?  You could also try venting, removing the column, capping the transferline off with a blank ferrule tightened properly, and then pump it down, wait an hour or so and try tuning. The tune will NOT be normal, but will give you an indication of the background.

Hi Paul thanks for the thorough response, 

The Rough Vacuum is 1.04E+2 mTorr and the High Vac is 8.705E-5 Torr

The turbo pump power reading is 21.5 W

There is one peak besides 42.10 that has grown its at 131 m/z and is about the same size as the now shrunken 69 m/z

There doesn't appear to be any leaks as it passes all tests and is holding pressure and the canisters are still fairly full and haven't been swapped during the time of the random peak showing up.

With varied column flow, when its turned down to 0.6 ml/min 219 m/z raises to 1 million~ counts while 42.10 shrinks back down but is still only slightly behind 219. When it is increased to 1.5 ml/min the counts for 42.10 remain about the same.

When Helium quench gas is turned it off there is no change. When the collision cell Nitrogen is turned down there is no change but when the Nitrogen is turned up to 1.75ml/min it does drop slightly to about 2.2 million counts.

The air and water check figures are - H2O 2.25%, O2 0.28%, N2 1.05%

I will be capping the column with a ferrule and tuning it this afternoon and will be able to get those results today as well.

Sorry about that here is the new spectrum. Its interesting that the peak at 52 is now showing when it wasn't there during any of the tuning reports.

So that shows m/z 52, not 42.

Click on the MS1 tab, and change Cutoff to 40, and the scan From 35 to  250.

and share a new screen capture.

Here is the new capture.

The filament was off again...

Sorry I don't know how that switched back. 

Safety. the filament will default back to off so that you have to choose to turn it on.

So there is about 1,175,000 counts of 42.1 m/z in there with the PFTBA off.  That's huge and certainly a problem that needs to be resolved. It's also a very unusual m/z - not sure I've ever seen just this mass in the background before and I've been doing this for a very long time.   

There are only so many places that can be coming from. The carrier gas or the collision cell gas are the highest possible choices. How long ago was the carrier gas tank replaced? Are the inline trap indicators showing problems? How long since they were replaced, too?

Safety. the filament will default back to off so that you have to choose to turn it on.

So there is about 1,175,000 counts of 42.1 m/z in there with the PFTBA off.  That's huge and certainly a problem that needs to be resolved. It's also a very unusual m/z - not sure I've ever seen just this mass in the background before and I've been doing this for a very long time.   

There are only so many places that can be coming from. The carrier gas or the collision cell gas are the highest possible choices. How long ago was the carrier gas tank replaced? Are the inline trap indicators showing problems? How long since they were replaced, too?

Both the Nitrogen and Helium were replaced within the last month or so. I haven't noticed any problems with our inline traps, the split vent trap I previously suspected of being an issue and was replaced Monday of this week. However the Big Universal Trap hasn't been replaced in quite some time would you recommend starting with that replacement?

Did the 42 start to appear ...in the last month?  I'd replace both tanks, purge the regulators as shown below, purge the lines, replace and purge the gas filters the same way as the regulators, and purge the lines between the filters and the GC all at the same time.

Hi Paul I purged the regulators and replaced the canister with no change to the tune. I also replaced our Big Universal Trap and Gas Clean Filter for extra measure also with no change to the initial autotune with the 42.10 peak still at around 2.5 million counts.

Do you have different tanks of helium and nitrogen - different lots or from a different supplier -  to connect immediately next to this instrument?  Then purge the regulators and traps and try again. 

I replaced the old canisters with new helium and nitrogen both from the same supplier, but I don't have spares at this time they should be getting delivered tomorrow and I can try again