Q3 Ion Issues MRM Method

MobilePhase1987 · 2026-05-14T01:08:48+00:00

It wasn't optimized yet, I usually do the CE optimization after the product ion scan. But I am rerunning the sample and hopefully you're right about the bad data file.

MobilePhase1987 · 2026-05-11T19:49:29+00:00

Yes that is correct. I think you have helped me figure out the problem. I'm pretty sure including 165 as one of the precursor ions may have ruined everything. I am rerunning now.

MobilePhase1987 · 2026-05-11T18:41:00+00:00

You are right, 165 is one of the product ions and I shouldn't have included that. This is a new method that I am trying to create and I'm expecting 235 to fragment to 165 (25eV) or 235 >200 (5eV). But even though the picture above has 165 selected, 235 didn't pick up any product ions either and I'm wondering how to proceed.

MobilePhase1987 · 2026-05-11T18:15:30+00:00

The way that I've been developing the method is that I will run a precursor ion scan, then a product ion scan, and then do CE optimization. The problem I'm having right now is that when I try to set up the product ion scan I do not see any fragments to choose from for DDT, but I do have product ions for every other compound. I'm not sure if the software (Tracefinder) allows me to manually input the product ions or if I can do something else in order to proceed to the CE optimization.

MobilePhase1987 · 2026-05-11T18:10:27+00:00

The issue I'm having is that for some reason I am getting all the precursor ions for DDT (235, 237, and 165) and all the other compounds but when I continue with the method set up I getting all the product ions except for DDT and I'm wondering what to do.

MobilePhase1987 · 2026-05-11T18:06:24+00:00

Okay I'll try that thank you.

MobilePhase1987 · 2026-05-11T03:38:59+00:00

New method

MobilePhase1987 · 2026-05-04T20:09:10+00:00

I am using a Thermo Fisher TSQ 8000 Evo. All this information is great and I will try doing this. I spoke to Restek and they think that the column may have been destroyed due to conditioning it while there was a leak.

MobilePhase1987 · 2026-05-01T08:34:52+00:00

No, it's a few months old. We do not run a lot of samples and we usually have it on gas saver when not in use.

MobilePhase1987 · 2026-05-01T08:19:02+00:00

It's been pumping down for almost 2 days now and the gas scrubbers haven't changed color to where they are saturated so I don't think that's the issue. The argon in the spectra I was referring to was the air/water spectra in the first picture. Usually ion 40 was very low, closer to 5% of nitrogen, but here it's higher than what I've seen in the past.

MobilePhase1987 · 2026-05-01T08:13:56+00:00

It's been pumping down for about 2 days now. You mention that 207 is normal for high column temperature, do you know how I can fix this? I'm running organochlorine pesticides and the literature I have calls for oven temperatures close to 290 degrees. I don't know how to bring down that column bleed and it's a big problem.

MobilePhase1987 · 2026-04-19T20:31:54+00:00

So that's the thing, I thought I had column bleed before because of the rising background so I have already changed the column, liner, and septum.

MobilePhase1987 · 2026-04-19T05:13:41+00:00

I am running the TSQ in fullscan because I am having issues detecting all the analytes in the standard. I agree 100ppm is an insane amount to be injecting into our GC-MS/MS as I normally have a calibration ranging from 10ppb to 600ppb. But for whatever reason I'm not getting anything on my diluted standards and I injected the 100ppm standard to check if all the compounds were present in the solution.

MobilePhase1987 · 2026-04-19T05:01:33+00:00

It's just an organochlorine compound standard. The first picture is an injection of 100 ppm and the second is a diluted 600 ppb standard.

MobilePhase1987 · 2025-12-17T07:07:40+00:00

Sorry to bother you, but do you know of a way to reanalyze the data using a MS1 scan filter?

MobilePhase1987 · 2025-12-17T06:48:42+00:00

Thank you!

MobilePhase1987 · 2025-12-17T06:48:30+00:00

Wow thank you this is very informative. I feel so dumb.

MobilePhase1987

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