Chromatography Forum

I've been working on getting an old CTC PAL/6890N/5975C combo up and running (sat in a room vented for the better part of a decade), which I've finally done but I'm having sensitivity issues I'm trying to diagnose.

I've cleaned the source, replaced filaments, all that good stuff and when I go to autotune, the relative abundance of the 219m/z PFTBA peak sits right around 40% for both filaments (the recommendations I've seen say it should be >65%, on our other 5975 it's usually >80%) and the 502m/z peak sits right around 3% which is on the low end of recommended spec. My PI seems to think it's the electron multiplier, so mainly I'm looking for ways to troubleshoot that specific part without just replacing it (not currently in the budget). Also is there any way to know if the quad is fouled without opening it up?

I'm venting right now to RE-clean the source and see if maybe I gummed up the filaments, but my bet is on the EM as well.

It could be a corrupt tune. Load a fresh one from the software, usually found in a separate folder under the 5975 folder.
As long as you are opening up the ms, try turning the EM cone 30-45 degrees. This changes the ion impact point.

Normally the EM going bad will affect all masses nearly equally, so having a loss in mid mass shouldn't be EM related. If the autotune sets the EM volts below 2000 then the EM should be ok. 2000v is high, and a new EM horn will tune near 1000v, but there should still be life left in it at 2000v and 69m/z abundance over 300,000.

Dirty quad can cause low mid mass but normally quad contamination causes peak width instability instead and all masses are affected. The HED can become dirty and reduce some signals too.

How long has it been under vacuum and heated? After being at atmospheric pressure for so long, it can take a week under vacuum and heated to get all the water and air out of the metal and ceramics in the analyzer, which causes abundance problems at mid mass.

I just went back and looked at the tune plots and it's been tuning at just under -2000v, the Agilent manual says it needs replacing once it hits -3000v so I'm guessing that's not the issue either?

I reassembled and pumped down last summer and it's been heated and under vacuum pretty much constantly since then but hasn't been used cause we were having issues with the CTC.

I got everything cleaned again (filaments were good), rotated the EM about 30 degrees-ish as was suggested... it's pumping down now (or trying to anyway), so I will try to restore the tune file and re-tune and see what happens.

If it has the turbo pump a 5975 should pump down and be at operating vacuum in less than 10 minutes, maybe 15 at most. If it is taking longer than that, make sure the column flow is not above 2ml/min, if it is less than that, then you need to check for leaks if it is pumping down slowly.

So there seems to be some weird glitch where the software doesn't recognize when the diffusion pump turns on, so I sat there for an hour waiting for it to turn on after I knew it was warmed up..... closed the software, opened it back up and it was already down to 3e-5 torr (probably had been for a while)

So I re-ran the autotune and it's up to 65% 219m/z and 5% 502m/z, so some combination of cleaning everything and rotating the EM seemed to do the trick. Will run a sample some time tomorrow to see if I get better response.

Thanks for the tips!

Yes, I've found that Tune and Vacuum Control can be a bit "buggy" when it comes to reporting the diffusion pump status.

In my experience, it takes 1-2 hours for a diffusion pump to get a 5975 down to a reasonable pressure, even though the dialog box says 45 minutes...

Also, once a pump-down cycle has completed, the software will prompt you to allow 2 hours for the system to equilibrate. Any time I've broken vacuum, whether it's been open for 10 minutes or for a weekend(there have been very few times mine has gone longer than that) I give it at least ~12 hours and preferably more like 24(i.e. at a minimum wait until the next day to use it). I've found that the results just don't look good otherwise.

I have the same problem with diffusion pump status on a 5973 that is running version E of MSDChemstation. Sometimes it take a whole day before it will report as being at temperature.

I try to do maintenance on Friday and then tune and calibrate on Monday so everything is good and stable. You can calibrate after a few hours, but you will be doing it again in a few days as things settle in and the tune shifts enough to throw off the calibration. After a few days though you are good to go for a long time.

Yes-I agree on that. I generally won't run a tune or try to do anything until I've had at least 24 hours under vacuum.

Unfortunately, the "weekend" thing doesn't work for me since I often have grad students(and PIs) upset regardless of how much notice I give about down time. There's always something that "has" to be run right away, and I'll get bugged all weekend with "is it ready?" if I bring it down on a Friday and say not to use it until Monday afternoon...thus it's better for me to do it early to mid week so that I can monitor it and make sure no one uses it and then complains about the results(or have to deal with emails/texts/calls all weekend even though I'm not in).

I REALLY wish my my Saturn 2100 wasn't beyond economical repair...at the moment we only have one department owned GC-MS.

So I re-tuned today after letting it vent over the weekend to make sure it got a good tune and it still seems to be in good shape.