Chromatography Forum

Dear All,

Thanks for looking at this topic. I need some help with our GC-MS. I am analysing 11-dehydro-thromboxane B2, the metabolite of thromboxane B2. Following a standard derivatization procedure, I injected the PFB ester, TMS ether derivative of 11-dehydro-TxB2 to GC-MS, however, I couldn't detect any peaks at all. And the baseline was somewhat high and it dropped very suddenly at about 2-3 minutes at the end of the run (total run time is 20 mins).

I wondered whether it was due to the GC-MS. Following a maintenance of chaing the liner, the sudden drop of the baseline was still there. And this time, I tried some other compounds which I successfully identified (8-iso-prostaglandin F2a etc), but they all couldn't be detected.

Any one has experienced such problem, and has found a solution? Please help me!

Do you see any peaks in chromatograms at this point?

There are many possibilities, so I will give you some questions that lead to finding some common problems:
- Any indication of leaks in the GC?
- Do you have adequate pressuer in the carrier gas supply?
- Did you change the septum on the GC when you changed the liner?
- Do you have a step in the GC method that runs the filament off at the point where the baseline drops?

If you will list the conditions from your method, type column used, and solvent used in your injection, this may help someone to identify your problem.

Thanks Don_Hilton for your reply.

Acturally, I could see several peaks at retention times after the baseline had dropped (later than 18 mins), which was at the end of the run. However, the right peaks should appear at between 12 to 14mins.

Following is the conditions of GC-MS:

Selected ion monitoring was performed using Agilent 6890N Network GC system and Agilent 5973 inert Mass Selective Detector instrument interfaced with a Chemstation computer system. A programmed temperature vaporization inlet system in solvent vent mode was applied to inject large volume of analytes. The gas chromatograph was equipped with a 30 m x 250 μm I.D., 0.25 μm film thickness, Supelco SPB-1701 fused-silica capillary column and operated at 280°C. The column temperature program runs from 80 to 235°C at 34.00°C/min then from 235 to 280°C at 10.30°C/min. Helium was used as carrier gas at a constant flow rate of 1 ml/min, and methane as the reagent gas. The ion source temperature was 150°C.

The PTV inlet uses septumless head. We did clean it and change the Teflon ferrule.

As regards to leaks, I doubt this. The loss of detection only happened recently.

And I use isooctane as the washing solvent, the compound was in BSTFA solution.

Thanks Don_Hilton for your reply.

As regards to leaks, I doubt this. The loss of detection only happened recently.

I don't follw the logic here. You need to check for leaks with a leak seeker.

You have quite a complex set up and method, in addition to what Don asked, are you sure that you have CI gas at the right pressure ?, check also that the syringe is not blocked and that it is actually sucking up sample.

Peter

I would suggest that you inject a high level standard in scan mode. You will know how many peaks to expect and what masses should be seen. If the peaks are present, but late and smaller than expected -- it is most likely a leak in the inlet (or a malfunction in a complex inlet system).

And, before that I would use a leak sniffer to check for leaks. They have a way of not being there one day and being there the next.

Thanks for the suggestion. I will follow.

I am very sorry for the wrong assumption. I am not very experienced with gc-ms. The forum is one of the way to learn from you.