Noise in A/W Check, Tune Failure, and more

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

26 posts Page 1 of 2
Background: I'm at my wit's end with this system. Any help would be greatly appreciated. My first project at a new job is to get a 3-yr old Perkin Elmer GC/MS up and running that has mostly been sitting unused (but on, under vacuum). The ultimate goal is to set up Method TO-17 for VOCs in air.

Instruments:
ATD= PE TurboMatrix 650
GC = PE Clarus 680
MS= PE SQ 8 T

Initial issue: High nitrogen in a/w check (~90% of mz 69). N2:O2 was typically about 5:1, but other ChromForum posts suggested this could still be an air leak, just the scrubber is removing some oxygen. Note: with MS capped, no leak is seen. Pic is with MS not capped: https://alleghenycounty-my.sharepoint.c ... w?e=lG5UX2

Initial Fix Attempts: I won't list everything, but basically I did everything I could think of/read online about 3 times. Multiple people leak checked everything multiple times with leak detector and canned air. Replaced/tightened connections over and over, changed tanks, everything. PE applications specialist suggested many things to try, none of which worked. Were due for PMs on all three instruments anyway, so service call was made.

Service Call Actions (performed by/with engineer):
ATD: failing "column leak test"--> tightened all ATD connections --> column leak test passed consistently;
-Replaced o-rings and filter in sample tube holding assembly--> tube leak check passes consistently.

MS: Capped MS, confirmed a/w check is decent with cap;
-Changed pump oil;
-cleaned source (I had cleaned it about two weeks prior);
-filled ref gas vial and flushed valve lines for air;
-reinstalled the column into the MS with a fresh cut and fittings. Here's where the fun starts...

Resulting A/W check (see pic): (In addition to there still being high nitrogen) Lots of noise around all masses checked. Neither Autotune or mass calibration will complete. We receive this error: "Unable to set appropriate values for low/high mass resolution". https://alleghenycounty-my.sharepoint.c ... g?e=xYsJnL

Service Call Fix Attempts: vented, reassembled the source--> no change;
-pumped down overnight (it was the end of the day) and ordered some parts;
-the service engineer replaced the high energy power supply--> no change;
-replaced the head amp board--> no change;
-replaced the EM--> no change.

End Result: The engineer had to move onto another customer and is sending a main board for another engineer to replace.

Has anyone experienced anything like this? Any ideas of what could cause this to randomly happen after super routine maintenance (performed by a service engineer to boot!)? Help, please!!
I'm not familiar with the PE mass specs but I notice in the first pic the levels are given in % and in the second they are in counts(very high counts in the 10,000,000+ range).

What were the peak heights in counts originally?

Also you said a new Electron Multiplier was installed, but I see in the second pic it is at 1400 volts. I know when I install a new multiplier in an Agilent it will normally run in the 1000-1200 range, maybe the multiplier is set high giving too much background and saturating the peaks causing failures.

Another thing to check is to see if the column is inserted too far, I know on an Agilent it will cause a lot of noise and tune problems if the end of the column is too far into the source.

The original problem before any fixes was just too much air, but you couldn't find a leak. What is the split vent flow on the inlet if it is a split/splitless injection port? If it is too low, air can diffuse back into the port and appear as a leak but you won't find a leak using a leak detector.
The past is there to guide us into the future, not to dwell in.
Thank you for your response, James!

Unfortunately, I don't know the counts for the first picture. I'm also only familiar with Agilent systems, and I couldn't figure out how to switch the view to counts. The SE showed me how to change it.

Good point about the EM! Below are the counts with EM at 1000 and 1200. The noise goes away at these settings, but so do the peaks (mostly at 1200 and completely at 1000). That doesn't seem right to me. What do you think?

(Honestly, I'm concerned about the EM generally. Before the service visit, autotune put the EM at ~1900...on a 3yr old instrument that's barely been run. Do you agree that's odd?)

EM at 1000
mz 69, 18, 28, and 32 all read 1e0

EM at 1200
mz 69= 4e6
mz 18= 1e0
mz 28= 7e6
mz 32= 1e0

I'll vent today to check if the column is inserted too far. The engineer used the "push it in till it hits, then pull it back" method, which I'm sure is adequate, but I prefer to measure.

The injection port for this system is a direct transfer line from the thermal desorber. The outlet flow from the ATD (which I'm thinking is the same flow to the inlet side of GC column?) is 40mL/min. This is my first experience with an ATD, so I may be thinking about this incorrectly? After reseating the column in the MS and checking a/w, I'll try upping the flow and seeing what that does.
Ok, second update/clarification.

I vented and found the column had been installed about 3cm too far into the MS. I reinstalled the column at the manufacturer recommended length.

After pumping down for 45mins, this is the A/W check. I only upped the gain to get a visual of the signal (doesn't change the counts). https://alleghenycounty-my.sharepoint.c ... A?e=HtvYwk

So it wasn't the silver bullet I hoped it'd be, but still something to be corrected.

As for the column inlet flow, I looked more into the ATD settings. I found the column flow was set to 1.0 mL/min. The Perkin Elmer app note I have for TO-17 suggests a column flow of 1.8 mL/min, so I upped the flow to this. Do you think that difference could be significant?
Kacie wrote:
Ok, second update/clarification.

I vented and found the column had been installed about 3cm too far into the MS. I reinstalled the column at the manufacturer recommended length.

After pumping down for 45mins, this is the A/W check. I only upped the gain to get a visual of the signal (doesn't change the counts). https://alleghenycounty-my.sharepoint.c ... A?e=HtvYwk

So it wasn't the silver bullet I hoped it'd be, but still something to be corrected.

As for the column inlet flow, I looked more into the ATD settings. I found the column flow was set to 1.0 mL/min. The Perkin Elmer app note I have for TO-17 suggests a column flow of 1.8 mL/min, so I upped the flow to this. Do you think that difference could be significant?


Flow shouldn't make problems for the sensitivity and noise unless you are exceeding the amount the vacuum pump can remove from the chamber. As long as the vacuum is in the green you should be ok on that.

Counts in the e^6 for 69 are good on an Agilent, but can't know for certain on the PE. Since the 28 counts are higher than the 69, it would show there is a leak somewhere. If you use a no hole ferrule at the inlet instead of the column does it give the proper reading? If so then the nitrogen is being introduced before the MS and the problem is elsewhere.

One big thing to check is to make sure it is a Helium tank instead of Nitrogen tank attached, since they both have the same connector (inert gas) they can be interchanged accidentally. I know because I have done it before.
The past is there to guide us into the future, not to dwell in.
Yes, my vacuum has always been good. I mentioned upping the flow more in response to your idea that too-low-flow could cause air to diffuse back into the system than as a solution to the leak issue.

I agree there's still a leak somewhere (though being unable to tune, the true proportions might be different than they appear?).

I've capped the MS inlet with a no hole ferrule 3 times now (once with the engineer) and a/w check gives a proper reading each time. The GC, thermal desorber, and gas lines have been leak checked many times (with detector and canned air) by multiple people including the engineer. No one has been able to find anything. I've also replaced the GC connections many times. We have also switched from a direct tank to a shared manifold system, and so replaced some of the gas lines/fittings as well.

I can confirm that we are using a helium tank. I checked the tank itself, and I can see helium in my a/w check when I look for it.

What are your thoughts on the EM info I posted?

Thank you again for working on this with me!
Kacie wrote:
Yes, my vacuum has always been good. I mentioned upping the flow more in response to your idea that too-low-flow could cause air to diffuse back into the system than as a solution to the leak issue.

I agree there's still a leak somewhere (though being unable to tune, the true proportions might be different than they appear?).

I've capped the MS inlet with a no hole ferrule 3 times now (once with the engineer) and a/w check gives a proper reading each time. The GC, thermal desorber, and gas lines have been leak checked many times (with detector and canned air) by multiple people including the engineer. No one has been able to find anything. I've also replaced the GC connections many times. We have also switched from a direct tank to a shared manifold system, and so replaced some of the gas lines/fittings as well.

I can confirm that we are using a helium tank. I checked the tank itself, and I can see helium in my a/w check when I look for it.

What are your thoughts on the EM info I posted?

Thank you again for working on this with me!


The EM at 1200 seemed to give normal levels.

Maybe you should tune with the no hole ferrule in place then install the column and run with the same tune for air and water check ( you may have already thought of this though). That would at least have you checking for leaks with a known good tune so you get proper ratios.

It sounds like the leak though is somewhere in the GC or Thermal Desorption unit. I would guess the Thermal Desorption unit just because that is where the most complexity is and there are probably places it can leak that are difficult to test. That always seems to be what happens to me, the most difficult to test place is where the first leak occurs.
The past is there to guide us into the future, not to dwell in.
Purge all your He lines going into the GC and the thermal desorber.
Cycle the thermal desorber a couple times. Run a couple blank tubes.
This should help bring down your N2 levels.
Thank you both for your ideas!

Today I capped the MS and tried to run an Autotune and mass calibration (previously neither would complete). The mass calibration consistently completes.

The autotune has run to completion a couple of times, but fails to complete most often. Literally nothing changes between autotune attempts so it make no sense to me why sometimes it would pass and sometimes it would fail. Do either of you have any thoughts?

I flushed the helium lines today, but of course I won't be able to see if this helped with the nitrogen issue until I have a reliable tune.
Kacie wrote:
Thank you both for your ideas!

Today I capped the MS and tried to run an Autotune and mass calibration (previously neither would complete). The mass calibration consistently completes.

The autotune has run to completion a couple of times, but fails to complete most often. Literally nothing changes between autotune attempts so it make no sense to me why sometimes it would pass and sometimes it would fail. Do either of you have any thoughts?

I flushed the helium lines today, but of course I won't be able to see if this helped with the nitrogen issue until I have a reliable tune.


I don't know enough about the PE system to know how it autotunes, sorry. I know with Agilent you can wipe out the old tune and start from defaults, but I don't know if PE does that or not.
The past is there to guide us into the future, not to dwell in.
Meaning you think the tune file may be corrupted? I remember that used to happen with my more mature Agilents. I can look into whether that is applicable to PEs. Thanks!
Kacie wrote:
Meaning you think the tune file may be corrupted? I remember that used to happen with my more mature Agilents. I can look into whether that is applicable to PEs. Thanks!


At least on the 5971 I use at work(the ones I maintain don't generally do this), a full autotune sometimes will crank the EMV up crazy high trying to get the 502/69 ratios it wants, and then will error out of autotune when the EMV hits ~2300 with "there was an excessive signal level." I don't know why this particular instrument has this quirk-when it happens I click "reset defaults"-the defaults are actually in the manual, but that's a quick and easy way to do it.

Surprisingly enough, the tune actually looks passable-if not great-at defaults. From there, I usually jump the EMV up to 1494, which is a typical "good" tune value for it, tweak the peak widths, and then use the repeller voltage to get the 502/69 ratio in the ballpark. I then use "quicktune" rather than risking a full "autotune"-it's generally happy with the peak widths I set, but quicktune does tweak the EMV and a few other parameters to get the ratios right-it only seems to work if you're already close.

Unfortunately, I can't offer any help on your PE instrument. I've never had the (mis)fortune of working with a PE GC-MS...the only chromatography experience I have with them is with a pair of HPLCs that I'm desperately trying to replace now with factory refurbed Agilent 1100s. I have a decent number of recent PE instruments(FTIR and fluorescence in addition to the HPLCs) and in general I'm not overly fond of their software.
Thanks for sharing your experience, Ben! I think you might be onto something about the autotune setting the EM high. Since I started here the EM has been tuning way higher than I'd expect for it's age, even the new one installed by the engineer last week. Something is going on there, but I don't know enough about the tuning process to know what could be affecting the EM voltage this way.

Unfortunately, I could not find a "reset default" type setting in this software (I agree this software is a misfortune haha). However, I found a way to set the maximum final EM voltage. I tried setting this to 1350, but still the tune would not complete. Received the same error of "Unable to set appropriate values for low/high mass resolution." I can manually tweak the tune to get ok values, but it very much worries me that the MS cannot complete an autotune.

Yesterday I tried using older tune files (even deleting the newer "bad" ones to avoid the software using those pathways). No change.

An engineer is coming today to install a new main board, so we'll see if that has an effect.

Thanks again!
Can you check to see if your nitrogen is coming from your helium supply?

I have had a bad batch of helium (when the supply was restricted) with nitrogen (argon too) in it. A quick switch to a different tank, not filled at the same time, made it obvious.
Steve, yes switching to a fresh tank was one of the first things I tried in my original search for the leak. And it was definitely from a different delivery. Thank you for the idea though!
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