The best way to troubleshoot these machines was to split the problem in half again and again until you found the part that needed to be cleaned, repaired, or replaced. The way to do that was to run different known chemicals with their own known signatures through the machine again and again. For example, you could run a single chemical (maybe ethanol - I honestly don't remember which ones at this point) and see if it goes straight through the GC and gives you the peak you expect. If it doesn't you could look at the result and see if the timing was off (indicates something with the GC or gas flow) or if the peak was wonky (indicates something with the MS). And then you just keep going. (Sounds a lot like unit and integration tests right?)
Applying that same strategy works wonders for data pipelines as well. Is it something with the extractor or loader (or god forbid Airflow)? Break it down and go from there.
My only nit on this is that while bifurcate is technically accurate (or is it actually?) it feels unnecessarily complex sounding for folks learning this skill.