Issues with high background with 5975C

After some very severe foreline pump backflushing into an MS, our thermal desorption-GC/MS system has shown noisy high background chromatograms - not surprising. Looking at the ions, they are generally spaced by 14 amu which seems to be indicative of foreline pump oil.

I have cleaned the ion source thoroughly and wiped off the large inner surfaces of the MSD with methylene chloride, but the background is still there and has not diminished even slightly. Baking out the system has not worked out either.

The autotune seems pretty good (with more peaks than usual though as expected from an oil contamination), and is mostly unchanged when changing filaments. 

Here you can see an example of a recent chromatogram of what should be a 'blank run' - usually the baseline would be below 10000 counts and have a distinctive baseline jump from 1 min to 5.5 min from the thermal desorption instrument:

The most recent autotune:

Any ideas? Is this just a super dirty MS - and what can be done in that case beyond what I have done? 

Or might there be other issues? Can one of the other parts be damaged from the contamination and in need of replacement or cleaning?

I do wonder if there might be multiple issues coming into play here. Before the backflushing of oil, the signal did suddenly start to become super noisy.

Any help is appreciated! 

  • This is a diffusion pump system?  Was it rough pump oil up in the hose and into the diffusion pump or diffusion pump fluid up inside the analyzer or both?  Diffusion pump fluid is Santovac 5 which is soluble in Acetone and Light Aromatic Solvents (like Toluene).  It is much heavier, 446, 447, 77, than rough pump oil.

    The rough vacuum is not great at 80.324, it should be typically less than 50. Was the rough pump damaged?  Was it replaced?  How about the rough pump hose?  Was the diffusion pump removed, drained, and refilled with fresh diffusion pump fluid?  If the fluid level is too high or too low, the pumping efficiency is compromised.  If there is rough pump oil residue in the diffusion pump that would be continuously contaminating the system.

    If either rough pump oil or diffusion pump fluid got everywhere - then the analyzer manifold, analyzer side plate, ceramic source connector board, quad, quad contacts, quad end cap ceramics, electron multiplier, HED, and the ion source are all contaminated and would need to be cleaned or replaced.  The ceramic source connector boards and quad contacts are partially ceramic insulator which cannot be cleaned. The quad end caps at both ends are ceramic insulators which cannot be cleaned.

    To get this system back to ultra clean is going to be difficult and expensive.

  • What does your 10-700 scan look like at your max isothermal temp? Had this happen and we also cut the column on the detector side and baked out at max temp overnight after giving the analyzer chamber a DCM bath. Might have replaced the multiplier too. If you have a known good column you could install it and try another blank run.

  • Thank you for your thorough response!

    Yes, a diffusion pump system. I could visibly see the rough pump oil flush up, and my colleague who did maintenance recently on the diffusion pump said that it was very full with oil. I am unsure whether diffusion pump oil entered the analyzer.

    The rough pump was probably damaged. I have switched it out now with a functional one + a new hose, and the vacuum is now below 40. The diffusion pump was drained and refilled. 

    I fear however it is a lost cause. I have tried now multiple times to clean the parts I feel comfortable with (and some I don't). There is little to no difference in the background signal after the cleaning. 

  • Did you remove the diffusion pump, take it apart, empty the contents completely, wash them all with something like toluene, reassemble it with new diffusion pump fluid filled only to the top of the "cold" mark - if you didn't take it all apart and any rough pump oil residue is still there, that would be the next step. 

    The quick expensive way is to clean the pump and manifold and replace the analyzer.... the 5975C analyzer G3170-65775 is $22,594 USD as of 28Jun2024. 

    Your last tune posted above - the quad looks like it's good, surprisingly. The tune ion peak shapes are still symmetrical. Except for the extra peaks the tune is pretty fine. So maybe time under vacuum or vent, wash with solvent, pump down wait, and repeating that a number of times will get it down.  Use grey scotch-brite pads on the manifold, turning them often, scrubbing front to back, and wipe with solvent dipped lint-free cloths multiple times. These parts are manufactured and not ultra clean to start with so even oil contaminated parts can gets cleaned, at least most of them can.

    How's the background without the PFTBA on?  Will this interfere with your data or just be a nuisance?

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