Raising Gain Factor vs. Lowering Threshold - Increasing Sensitivity on a GC/MS

An experiment. Set the threshold to 40, right about the system electronic background - and run a blank or a low standard.  Then In MassHunter Qualitative Analysis, open a data file. Look at a spectrum immediately before or after your "certain compounds" peaks. This example below is a spectrum right before the first peak, Dodecane, in Sample A on a 5977 EM gain 1 which resulted in a run EMV of 1195.6 and run at a threshold of 75, the lowest brown line. Any ions lower than that have been thrown away. If I set the threshold to 150, the green line, or 300, the purple line, I lose the ions below that.  Even at 300, this instrument running in these conditions would have twelve ions in the background.  You want every TIC data point to have some data in it. 

But if I set the threshold to 300, a very valid setting for this system, and my primary quant ion in my peak of interest is 140, then the 140 will not be seen until it gets to 300, right?  That may be fine, but if you're pushing the sensitivity limits it also may be insufficient for that ion on this system.  On this system, a threshold of 75 is not bad at all - there are 46 ions shown and the baseline is, at this time, 4,000 to 6,000. TIC below.

But on some systems run this exact same way, the baseline at that point might be in the thousands or higher with hundreds of ions per spectrum. Later in the run on this system the baseline is about 20,000 and each spectrum has 94 ions.

So there's a unique-to-each-instrument balance to be found between gain, EMV, threshold, and the necessary sensitivity, baseline, and quant results that changes over time with tuning, use, maintenance, and consumable replacement.  In my experience, most operators set a low threshold and tolerate a high TIC baseline and then worry about the high baseline. Worries and perceived issues have been solved both by lowering and by raising the threshold setting.

Let us know how the experiment goes....

Apologies for the late response but I do appreciate the detailed and helpful response.  It has been a long and drawn out experiment with a lot of data to comb through.  It seems like the default threshold of 150 (for this instrument) is ideal.  I have found that adjusting the gain factor alone as well as various method parameters in method edit view is enough without manipulating the threshold too much.  It is interesting to note - the instrument was down for quite a while this year for a software upgrade that took months to complete - after the new software was installed, the instrument responds to a much lower gain factor than what was previously used.  Regardless of gain factor setting used, primary quant ions dictated in EPA 624 for 1,2-dichloropropane (112) and 1,2-dichloroethane (98) do not get integrated by Quant for whatever reason.  When I open the data file in Qual at the lowest cal level, the primary ions are there and ratios look agreeable, but not integrated in Quant.  Any feedback in regards to that is helpful, but for now I am using them as qualifiers and I thank you for the help thus far.