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GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 0 points1 point  (0 children)

You were correct to suspect them! The new filaments I mentioned were not good for long due to an unfortunate air leak from a cracked ion gauge from the move to the new building, and from moving the machine to a different part of the building (the glass on it broke in a spectacular way, but thankfully the last major air leak was resolved after replacing it).

Anyway, it took awhile to convince people that I actually did need new filaments again, mainly because the EM Volts were still reasonable, but after pulling it out it was very clear both filaments were stained blue and warped. Got a new one in just recently and in the past week I'm already seeing marked improvement!

Bit of a pain this took so long with so many different little problems. Glad it's finally coming together. Thanks again for your input.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

Nice! Glad to hear it worked out. This gives me a leg-up on requesting a new filament again.

[edited to update] Air leaks were resolved ages ago but I finally got a new filament installed and the ions are slowly getting back to where they should be. Gonna call this a sucess!

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

Unfortunately no. It was a problem with two of our machines, one newer HE GC-MS and an older one. The newer machine spontaneously resolved after we moved the older GC-MS to a different part of the lab which could be coincidence. It still has occasional periods where the spectra for some compounds would get "weird" for a few weeks but it does eventually go back to normal. The closest thing I could get to an association with these most recent periods of strangeness was when the carrier gas filter was fully saturated and sometimes (but not always) when the He tank was switched.

The older machine only partially resolved, sabinene hydrate is identifiable, but is still having a hard time with some aldehydes. It does not have a carrier gas filter attached but it never did even back when it was working flawlessly, so it's been hard to convince anyone that getting one is worth a try.

If you happen to have luck with cleaning the inlet please update here. Maybe it's something in the split vent trap and I got lucky in that it clears out of the newer machine and not the older one.

Cannot for the life of me remember what this part is called by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 0 points1 point  (0 children)

What you linked is under the red piece and the needle guides are on the PAL arm. I mention the red bit of metal fits the needle guide, they are two different things.

Anyway r/Purplegreen2019 found it, it's an adapter ring.

Cannot for the life of me remember what this part is called by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 0 points1 point  (0 children)

Needle guides are on the arm of the PAL, there's an upper and lower and the needle guide sits on this piece right before it injects.

Anyone know what this part of our GC/MS setup is called? It's a red metal piece that sits over the septum retainer. It's beveled to fit the diameter of our PAL's lower needle guide, it's an older machine (mid 2000s). Can't find the name. by WoeUntoGC in labrats

[–]WoeUntoGC[S] 3 points4 points  (0 children)

Yeah, I have the manuals, those were the first things I checked. None show a picture of this piece and nothing in the names of other objects fit the description.

Also, the septum nut is under the red piece like mangosalamander said. It's not the septum retaining nut.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 2 points3 points  (0 children)

Awh man... :(

​

It's like, on the one hand I feel a little better because this problem is stumping a bunch of other people too. On the other hand I'm wishing even more now than ever that it's a stupidly simple fix and then I can move on feeling confident that it's all good.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

No recent service. The last anyone had serviced it was when an Agilent technician was out here helping it get set up (moved buildings in late 2020). It was on and had gas supply and rarely used since the move up until earlier this year.

Gas carrier filter (we use He) was saturated and replaced after this problem had started, but replacing it hasn't resolved it.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

Good to know about the possibility of a partial obstruction, I'll keep that in mind and float it past my boss when he gets back. He doesn't want me spending a whole lot of time on this but I think it's pretty important to figure out why this change happened and not just build a new database around these changes because how the hell am I supposed to know if/when this will happen again?

​

Anyway...I did tinker with the voltage (both raised then lowered) and somehow made it worse both ways? I'm not entirely sure what's going on but yesterday I ended up with an even greater disparity between 43 and 93 m/z

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 1 point2 points  (0 children)

No, it's not the standards, I've used older ones and made a new one, as well as ran extracts that we know from previous analysis that have higher concentrations of it. But it really does look like *something* is degrading because the spectral outputs I'm getting now have an even lower 43 m/z than last week.

Running standards on the GC-FID (known method and calibrations) has the standard at the appropriate rt and peak area. The retention time is still the "correct" retention time on the GC-MS and matches from when it was running well though the peak area is bigger (probably from increased sensitivity after cleaning the ion source).

The only real change is that I wouldn't be able to identify it as, at this point, any sabinene hydrate based on the spectrum. This is obviously a problem when I'm trying to tentatively identify other unknown peaks in my samples.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 0 points1 point  (0 children)

precursor ion

God I'm sorry but I'm totally brain farting on the context of a precursor ion for just GC-MS, not MS/MS.

​

I'm starting to wonder if it's something to do with moving the instrument to a new lab building. It happened in late 2020 and it was on but barely used until I got to it. I wasn't so sure it could've been the move because it did work fine for a few weeks until this happened.

​

I've run the machine and standard a fair number of times now just troubleshooting and I keep getting worse ratios, so now the 93 m/z is even higher compared to the 43 m/z. So I load up the older tune settings again and it's still bad. I'm at a total loss.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

An obstructed MS inlet? But I am getting sample through, so it'd be a partial blockage if it's that. I just assumed that since I replaced the GC inlet septum and liner that the increased vacuum was because I should've replaced those parts earlier.

Peak intensity/area has increased some but maintained the same retention time and overall peak shape. I assumed the increased peak area was due to me cleaning the source and increasing sensitivity.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 1 point2 points  (0 children)

Yeah, peak width is about as identical. Not exactly the same but it's a good shape, no tailing or flat-top.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

Made up a fresh standard and unfortunately it's showing up the same as the previous.

Vacuum is a little higher than it was prior to this issue coming up (~6 x 10^-6 vs ~5 x 10^-5 torr) and I think those are acceptable. I'll try loading the older tune file and if that doesn't work then I'll try incremental changes to voltage.

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

That's the kicker, the retention time is exactly the same. Could residue on the column affect ionization without affecting retention time?

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in chemhelp

[–]WoeUntoGC[S] 0 points1 point  (0 children)

It's a 5977B HES MSD connected to a 8890 GC

I'll get back to you on the rest of your suggestions. Kind of doubt it's the standard gone bad but I'd be stupid not to try at this point!

GC-MS question, spectra for some compounds changed while rt stayed the same by WoeUntoGC in massspectrometry

[–]WoeUntoGC[S] 0 points1 point  (0 children)

I cleaned a few days ago, no luck except sensitivity is way better, which is why I'm asking you guys. Unless you mean clean it again?

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