High base peaks and isotope ratio failing in GCMS auto tune

We have a GCMS(5975C, intert EI source) which had been out of order since long 6 months due to ALS tray issue. After we installed tray, we cleaned ion source, replaced filaments, cleaned inlet, vent line and replaced split vent trap cartridge. Then tune passed, but when solvent blank and standards run, baseline was very noisy, though we were getting Internal standard response.
We thought it may come from inlet or column. We cleaned inlet again, conditioned column, but it was same. Then replaced the column with a new one. Still it was same. Then again we cleaned ion source.
Then suddenly tune is not passing. 69 and 502 isotope ratio are failing. Baked MS 12 hours, but still it is same. I found base peak around 800 this time(when tune passed, it was 94) so I thought, detector might be dirty. I cleaned detector with ACN, but its still the same.

What else can be the issue for this high base peaks and the isotope ratio failing?

  • Please share the current autotune report. Check the easy/simple things too - PFTBA in the vial not too high or empty.  Column flow 1.2 ml/min helium. Or try pulling the column out of the inlet, carefully press the end into the side of a septum to plug it, then wait at least ten minutes and try tuning.  The results with no column flow will not be truly normal but will tell you if the system is at least operating.

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