Chromatography Forum

We have a Agilent 5975C MSD (GC MS). Around 4 months ago, I suddenly found out one day that there was no baseline when I was running a sample. I tried to autotune it but it said "Tune action stopped: cannot achieve constant peak widths". I called agilent tech guys and they asked me to clean the ion source , which I did but there was no change in the autotune. I tightened the transfer line / column nuts, cleaned the ion source again, replaced one of the filaments with a new one, changed the moisture and oxygen trap, replaced the vacuum pump oil, replaced an insulator in repeller assembly (which was broken) but ultimately, there was no change. The abundance for mass 502.10 is way low (7910), N2/H2O~107.11%. Did tune evaluation couple of times and the report says that the ratio of mass 503 to mass 502 is high (it is 13.37 instead of being somewhere between 7.9 to 12.3%). It also says that the base peak should be 69 or 219 and it is 131.00 and the possible causes include no PFTBA in the cal vial or large air leak.

Can someone throw light on this??? I would greatly appreciate any help regarding this matter.

Have you tried another tune such as stune or bfb. If those look ok then you have a corrupt auto tune. Call Agilent for instructions to restore the tune.

couple of suggestions (some might be too simple but just covering the bases)

1. Did you check to make sure your tuning solution is not low?
2. How did you clean the source?
3. What is the pressure on the MSD as of now (in relationship to this what is the size of your column and flow used)?
4. Have you tired taking the column out and plugged the transfer line and then tuned?

If the tuning solution is low you will most likely start seeing mass 18 and 28 be very high as well as a lot of background noise and peaks you would not normally see in a tune. Try going into the tune and vacuum control screen, click on file, then click on "restore previous tunes". Select a known good tune file. It will ask if you want to use this file, click Yes and try tuning again. Also make sure you don't have the wires running to the entrance lens and ion focus reversed.

Or load the default tune conditions and start there.

Thank you so much for all your suggestions. I really really appreciate all your time and consideration.

@willnatalie
1.I checked the tune solution and more than a quarter of the vial is full.

2. This is how I cleaned the ion source:
#cleaned using alumina powder and methanol mixture
#Sonicated source parts (1st with methylene chloride, then acetone, and then methanol)
#dried them at 100 degC for 15 mins
After fixing back the ion source, I baked the mass spec for 12 hours but still didn't solve the problem.

3. The pressure on MSDis 83 mtorr (size of the column is 30.0m, 250u; flow is 1.200mL/min)

4. I haven't tried plugging the transfer line directly but will try it today if the tune doesn't work.

@MX304
I double checked the wires and they look fine. I restored a previous tune file yesterday and could do an autotune. But the abundance of the mass 502 was pretty low (5493). Then tried restoring another tune file today and it worked well this time. But the problem is, the position of mass 69, 219 and 502 is now 69.30, 219.21 and 502.28. It seems llike there is a shift in the mass and because of which, the system tune verification failed.

@Consumer Products Guy
I called Agilent to find out about how to set the default tune conditions but they said that I need to restore a previous autotune (a good one from long back) and that would be a default tune file. Can you please let me know how to set up the default tune conditions??

Need more suggestions............

I called Agilent and they think that it might be due to some problem in circuitry that monitors the quadrupole. They are charging us a lot of money for an onsite repair as our system is out of warranty.

Any suggestions???

That is a possibility. When it comes to the quad's there is not much that can be done....

pending on where you are there are external companies the specifically repair only and could be a bit cheaper.


good luck!

We have a 5975C and have not seen this issue. However; we had a a 5972 MS which could not maintain constant peak widths. It turned out to be the top board. Once replaced all was well. We replaced the board which was quite easy. I think that now the board is on the side of the analyzer. The boards are are fairly expensive but you save on the service call. After changing out the board you need to dip the RF which Agilent should be able to help you with. Might be something to check out.

Another thing to do before resorting to a service call would be to give the HED a good cleaning. There is also a slight chance of the multiplier horn needing to be replaced depending on the age of the system. What is your multiplier voltage running at on your tune?

My 5975 started doing a similar thing, wouldn't tune or the masses were all over the place (174 varied from 173.1 to 175.2). The fix was a new ribbon cable. One of the wires was broken and barely making connection. It was discovered during replacement of another component when the cable was removed and reconnected the other way around. Then something else didn't work. Too bad it wasn't the first thing tried.

To restore your tune file look in c:\msdchem\mssetup\5975\ and copy the correct atune file (look at the side of your MS, where the RF box is on the side board. There will be a sticker with either pos or neg marked with an x. If its pos use atune.pu, neg use atune.nu. If you dont see the file extensions (just see 'atune') from within explorer go to tools > folder options > view > and uncheck 'hide extensions for known file types'.

Rename your corrupt atune.u to like atune.old and copy the new file to c:\msdchem\1\5975\ and make it atune.u rather than .pu or .nu

Then run your atune and compare the results to a good print out (that you store in a binder next to the instrument, right or you will starting now..) and see if they look "good" (no split peaks, repeller isn't maxed out, EM Volts is somewhere between 800-2200).

If that still doesn't do it you can try to dip the quads, let us know when you get that far.

We also had this problem once. Our result was that the filament wasn't broken but was slightly bend out of shape which was enough to cause problems. Maybe try changing both filaments and not just the one.

Otherwise I agree with the corrupt tune file