Ion at every mass

What is the complaint?  The tune shows 166 peaks - a typical number. Air and water are less than 5% of 69 - decent but not perfect. The tune numbers look pretty good. My only worry would be the precursor on 69. I would change the quad polarity to NEG, save the tune file, then tune again and see if the tune ion peak shapes are more symmetrical.

If you scan lower than 45 you will always see a bit of air/water. Maybe not much, but always some.  The 44 is pretty high, too. 44 is CO2 and is typically a very small percentage, 0.03%.  It is also seen coming from the graphite/vespel ferrule on the transferline.  

What is your acquisition threshold?   With your current electron multiplier setting and tune parameters it should be maybe 1000.... so that any peaks lower than 1000 are discarded.  That's sort of a typical number/range, too.  

Do you need to scan lower than 45? Most applications do not need to see peaks of interest with ions lower than that.

And let us know!

My concern is that it also shows up in the TIC. There is quite a bit of noise in the chromatography.

What is the acquisition threshold in your method?   With your current electron multiplier setting and tune parameters it should be maybe 1000.... so that any peaks lower than 1000 are discarded.  That's sort of a typical number/range, too.    As the system response changes with time and tuning, the threshold may need to be adjusted to compensate - a typical thing.

Current threshold is 500. I am building a duplicate instrument.

The EMV setting is probably a bit higher than it was when the method was developed. I would set the threshold to 1000 right now and it would not use the ions below the red line:  If any ions are near the threshold number and go up above the threshold and then down below it, the apparent total ion chromatogram may look like noise even though it isn't.

And do you really have to acquire data below 45 amu?  If you could change to scan 45 to whatever your current threshold would certainly make for nicer looking total ion chromatograms with lower baseline abundance.

There's nothing wrong with the instrument or the configuration.  The method needs to  be able to accommodate the minor changes that happen with tunes and system response over time.

Need ion 43. Current method scans 40-550. Acquisition method needs to be the same as the other instrument.