Loss of sensitivity on 5977 B

The tune looks fine. Did it just change from something lower and how did that look?   Does it look the same on both filaments?   98.1% 219 and 8.4% 502 on an Autotune, not an Extractor Tune, is high, but in the typical range.  In Atune if 219 gets higher than about 125% I start looking for issues.  Then I saw that your column flow into the MS is either 1.5 or 2.0 ml/min depending on how the GC is configured.  These high flows will alter the spectral tilt, the relative abundances. Turn the column flow into the MSD down to the optimal 1.2 ml/min, let it stabilize for a few minutes, and tune again.

What did the baseline and peak heights look like previously?  Has this been decreasing over time or just happened? If it just happened -- what else was done or happened?

The baseline is very low and the two peaks shown are very small. What is your Electron Multiplier setting in your method? Is it set Absolute, Relative, or GAIN ?  My first guess would be that the tune EMV has increased since the system was installed about May 2021 and the method developed but your run method's EMV has not.  Try GAIN 2 or 3...

Threshold 50 is about as low as possible as <50 is essentially only allowable electronic background.

Please share your results.

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Here's the info for the gain.. Have not yet had to adjust these factors, so can you tell me why this may need to be adjusted? Great information.

The typical background is very low but still detectable. This method in particular is used to quantify at very low concentrations and we're wanting to go even lower to ppb levels. I actually did compare ISTD areas and they are similar if I go far back enough. Here's a comparison between runs a couple of months apart. /resized-image/__size/1280x960/__key/communityserver-discussions-components-files/147/ISTD-compare.PNG

The reason why I believed there was a loss in sensitivity is because the TIC typically picks up on a very small but still noticeable peak that is no longer there (still found on SIM), and because the background dipped below zero. Recovery for this standard was around ~80% this time around with this background issue.

Before running, I changed the inlet liner and column. The column has been in use since last year and has previously run great. DB 624 UI 30m 0.25 mm ID. No other changes were made. The run prior to mine as well had a detectable baseline (different method and column). 

Those raw counts are super low. If you are having issues with seeing the low end bump your EMV, having responses in the hundreds of thousands isn't uncommon. Electron multipliers will age out over time and need replacement but that one is basically brand new.

The peaks look similar, essentially the same sensitivity. I'd look at the background on your older runs and the background now.  It could be that most of the previous background was one, two, a few, ions and they're gone now.   Was that small but still noticeable peak at 207 amu? --- column bleed?   What mass range are you scanning?

The Gain curve that the system uses is generated during the tune.  It might be that Gain 1.00 was always just this side of too low and now the tune has changed which changes the gain curve which makes it now definitely too low.  Low is typically good/clean.  For a test, turn the Gain to 2.00. The EMV will change and the background should change. If that's the case, that's typical.  Please share a copy of your latest autotune.