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.

Would you please share a screen capture in tune of the MS1 Scan with the PFTBA off and the filament on?  42 plus 131 has strange searches, so I wonder if there are other smaller peaks that will help find it.  There are certainly siloxanes with those ions so this very well could be column related.   

The tune with no column flow will not be normal.  The PFTBA can get into the ionization chamber easier with no helium molecules streaming out.

Please share the tune report, too. 

Forgive the ignorance but how do I go about turning off the PFTBA? I checked the level and it is still under the accepted level but that is unfortunately as far as my knowledge goes.

Go to tune, choose the Manual Tune tab. Make sure that Emission is checked - that will turn on the filament when needed, then uncheck the EI Cal Valve box and the PFTBA will not be turned on. Make sure that MS1 Scan is selected, then click on Acquire for one scan or Start for repeat scanning.

The filament will glow and then a spectrum will be displayed. Let it refresh a few times - five or ten seconds or so - and then click on the STOP button at the bottom. Do a screen capture and share that.

Buttons

Acquire This will do a single acquisition of a spectrum using the scan modes selected on the MS1 and MS2 tabs.

Start This will cause a manual tune to continually acquire data until the Stop button is pressed. The effects of changing parameters can be seen in the plot window.

Stop This will stop the continuous acquisition of data started with the Start button.

Capture This will perform a single capture of SIM or TTI data with parameters specified in the acquisition tab. The captured data will be shown in the plot window.

MS On Turn on the analyzer electronics. This sets all voltages and temperatures.

MS Off Turn off the analyzer electronics. This turns off the voltages but maintains the temperature settings of the source and quads.

Go to tune, choose the Manual Tune tab. Make sure that Emission is checked - that will turn on the filament when needed, then uncheck the EI Cal Valve box and the PFTBA will not be turned on. Make sure that MS1 Scan is selected, then click on Acquire for one scan or Start for repeat scanning.

The filament will glow and then a spectrum will be displayed. Let it refresh a few times - five or ten seconds or so - and then click on the STOP button at the bottom. Do a screen capture and share that.

Buttons

Acquire This will do a single acquisition of a spectrum using the scan modes selected on the MS1 and MS2 tabs.

Start This will cause a manual tune to continually acquire data until the Stop button is pressed. The effects of changing parameters can be seen in the plot window.

Stop This will stop the continuous acquisition of data started with the Start button.

Capture This will perform a single capture of SIM or TTI data with parameters specified in the acquisition tab. The captured data will be shown in the plot window.

MS On Turn on the analyzer electronics. This sets all voltages and temperatures.

MS Off Turn off the analyzer electronics. This turns off the voltages but maintains the temperature settings of the source and quads.

Here is what I have after waiting 10 seconds for it refresh.

Please select the box next to Emission and do it again.  This spectrum has the filament turned off.

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...