Agilent 5975 MSD Autotune Report Readings

Question

I have couple of questions regarding Agilent 5975 MSD (run on MassHunter) Autotune Report. Please see the attached. It looks like for m/z 69, 219, and 502, there are two sets of data on the report. The Abund and Rel Abund (m/z 219) numbers are slightly different between the two data sets. 
 
 I guess the two sets of data are collected at different times. Is it correct to say that the top set is collected during mass assignment and the bottom set is obtained during Scan mode (of all peaks across the set mass range)? 
 
 So when I evaluate the Autotune results and check 'Rel Abund', which set should I use? I found in an online teaching document by Agilent, it is recommended to use the top set, could anyone explain to me why? 
 
 Thank you very much!

paulsalverda · Answer

Thanks for attaching the tune report! The data for the tune ion peaks at the top and the spectrum below are acquired at different times. The abundances will be different. They change depending on the tuning, of course, but also on the amount of time the PFTBA valve is open, the time since it was last opened, and the room temperature, among other variables. The MS is doing a headspace evaluation of the PFTBA in the vial. When the PFTBA sits undisturbed for a while it gets to a stable pressure, then when the valve opens and the PFTBA gets sucked into the MS through the very tiny restrictor inside of the PFTBA valve, the pressure in the vial changes the longer the valve is open until it reaches stability again. This can be used as a troubleshooting tool sometimes. 
 Agilent GCMS systems are more stable than most people think. They also do not necessarily need to be at the extremely sharp end of perfection for most applications and even a little bit off of maximum sensitivity is not much. An automatic tune is not like searching for the very tip of a needle, it&rsquo;s more like landing somewhere around the top of a wide bell curve. Most applications don&rsquo;t need a system at the exact cutting edge perfect tune. They could be detuned by 10% to 25% and not miss anything at all. Stability is much more important than ultimate sensitivity. 
 Most folks tune their systems too often. One of the menu choices is "Generate Report", which uses the currently loaded tune parameters, acquires new tune ion peaks and a spectrum, and then prints the report for you to manually evaluate. This takes dramatically less time than a tune and does not change any parameters. If the Generated report looks essentially the same as the last actual tune report your system is good to go. 
 So your system: Autotune (atune.u) adjusts to get the 69 between 350k and 600k counts or so. It tunes to maximize 502. 5.8% on a system that's this old is quite good and certainly sufficient. Most folks worry too much about the relative percentage of 502. If it's consistent and better than 2.4%, the tune evaluation lower limit, it's fine. Higher does not necessarily mean anything if it is consistent tune to tune, week to week. The EM Volts setting of 1906 with the gain factor of 0.3769 and 112 peaks in the scan is just fine, too. Electron Multipliers work great until they need to tune above 2600V or so all the time. You'll notice that this typically goes down after you clean the source, which improves the ionization efficiency, the effects of the electrostatic charges on the lenses to the ions, etc. 
 112 peaks is very clean. There is a bit of an air leak, though 4.9% N2 and 0.8% O2 is about the 4:1 ratio in air. Oxygen degrades the column and is hard on the filament. It would be best to do a bit of digging around to see if you can reduce that.

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Agilent 5975 MSD Autotune Report Readings

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