Air/water check - Autotune vs separate Air/water check

Nitrogen in QQQ tunes is calculated from the oxygen level since the CC nitrogen is still on. In air, N2 is 78.084% and O2 is 20.946%.  Take the O2 relative abundance and multiply it by 3.72787 to get the N2 relative abundance in the tune and checktune reports.

The separate Air/water check is arguably more accurate since the CC nitrogen gets turned off and the N2 and O2 are measured, but turning off the CC N2 also changes the overall ion transmission of the system.   Always work to get your air/water as low as possible.  Many systems out there have nitrogen down at or below  ~1% of 69.

The HES design is optimized to run well between 1.1 and 1.3 ml/min of helium (0.7 and 0.8 ml/min of hydrogen). Outside of that quite narrow range it works great, but the spectral tilt, the relative responses of ions across the range, is different.  Bad different or just different?  Just different, especially since most all QQQ systems are used to acquire MRM data and not Scan data used for library search matching. As long as the response is sufficient and consistent run to run the relative responses for ions across the possible scan range doesn't matter.  At higher helium flow the data from an HES starts to look like there is an air leak but there isn't, so checking for air/water at higher carrier gas flows is not necessarily valid.  Now that you know that, though, you could make a measurement at 1.2 ml/min of helium carrier and get like 1% N2 and 0.5% O2, a pretty leak free system, and then turn up the helium carrier gas flow and do a measurement there and be pretty confident that measurement is probably OK and typical for your system.

and see:  What is a “High Nitrogen” Value and How to Identify Possible Causes and Solutions 

If I am understanding correctly, then the air/water check during the tune should be accurate for water and oxygen but may be off for nitrogen since that is only calculated. To get the true nitrogen value I would need to run the standalone air/water check.

When running at 1.2 mL/min (after the system has been pumped down for an extended period), my nitrogen level is reading just below 6% with the standalone air/water check. My oxygen value corresponds to the expected ratio in air. The nitrogen value is within the 10% acceptance limit, but since you say that most systems can reach below 1%, would that indicate I could have a small air leak somewhere after the oxygen/moisture filter?

Higher than calculated percentage nitrogen would only be from contaminated carrier gas or residual nitrogen from a new trap that has not purged out.

I said "many" get very low nitrogen/oxygen not most.  Your 6% N2 means ~1.6% O2. The O2 is the primary concern, not the N2, as O2 through the column damages it and O2 in the ion source degrades the glowing filament.  Percentage of N2 and O2 to the 69 tune abundance is a guideline, of course, as tuning changes response. Try to get the O2 as low as you can without going too far. There's a balance of time and cost in there somewhere.  

To go further, get the absolute O2 abundance with the PFTBA off. Don't change any MS parameters and go hunting. It's complicated as you can't change the column or CC flows without affecting the abundance. It takes time, a few to many minutes, to see a change if you touch anything before the inlet end of the column.

Do you have an electronic leak detector?  Using one of those is certainly better than overtightening all of the fittings.  Overtightened Swagelok fittings and column connections can leak. Turn off gas saver and set split to 60:1 or greater.  Gas Saver at 20 ml/min is barely sufficient.

Do you have one tank of gas for one instrument or is the lab plumbed?  Eliminate the lab infrastructure to test.  Do you have a tank from a different batch or supplier to try?  Is the plumbing all stainless or copper or a mix?  Has someone else overtightened all the fittings before you?  Does your configuration result in inlet pressure less than 5 psi? Are you using two columns with a Purged Ultimate Union or a splitter? How old are the gas traps?  Maybe do a plumbing bypass to see if the traps are part of the problem.

I have an electronic leak detector but didn't pick anything up at the fittings.

For turning off the nitrogen during the air/water check, I am only really able to do that through the EPC. I am running off of a nitrogen tank that is only supplying this one instrument but there is no shutoff valve at the instrument. I tried shutting it off at the tank regulator but after a few minutes the GC panel was still reading flow, possibly because the line from the tank is quite long and would take a while to clear out.

I ran the air/water check again with the gas saver increased to 60 mL/min as you suggested and this decreased the oxygen and nitrogen values by about half. bringing the oxygen down to 0.66%. There wasn't any change to water. It is still around 1%. Would you consider this low enough or is it expected that these values could be much lower still?

To answer your questions on lab infrastructure:
- Gas supply for N2 and He is from cylinders and they are only supplying this one instrument. There was an issue a few months back where the results of the air/water test were just outside of criteria and we changed the tank at that time but it didn't make any difference.
- Plumbing is all copper with brass fittings, no stainless.
- No idea about over tightening. I have only come to work with instrument recently so I don't know its extended history and haven't touched any of the fittings yet myself.
- The inlet is at about 17psi with the current configuration
- We have a purged ultimate union. The current configuration is: inlet > column > PSD > deactivated silica transfer line > MS
- Helium gas trap was replaced 6 months ago, I am not sure of the age of the trap on the nitrogen line.

For the air/water check you have to turn off the CC Nitrogen using the EPC module. Turning it off at the tank would mean that entire plumbing would have to be evacuated to vacuum through the EPC module.

In my experience, 20 ml/min of Gas Saver is insufficient. It's not much flow. I recommend 40 to 60 ml/min.  It sounds a lot, but 60 ml/min is only 1/2 milliliter per second coming out of the split vent and the septum purge.  

PUU with PSD.  Column 2 flow should be 1.2 ml/min into the ion source so column 1 flow should be a maximum of 1.05 ml/min. There must be sufficient difference, 10% to 20%, so that there is always forward flow from the PSD added to column 1 flow going through column 2.

PSD purge flow need to be 10 ml/min.  If the PSD purge flow is too low there will be air in the background.

Is the helium gas trap indicator changing color?  The trap on the nitrogen is probably a Big Universal Trap with no indicator. If you're worried, add an indicating oxygen trap to the CC N2 line after the Big Universal Trap.

If reducing helium use is a priority, buy a Helium Conservation module for the GC using nitrogen or hydrogen during all the time the instrument is not being used.