MULTIPLE PEAKS AND BACKGROUND SUBSTRACTION CLARUS 500 GC MS

[Francisco Franco]

Good evening everyone:

I am new to GC-MS and I would like to know how likely it is for multiple peaks to appear for a single mass. Some days ago I realized that I got two peaks for a Thymol Standard solution (just one compound). After asking Turbomass to display the chromatogram for the m/z 135 only, both peaks remained.

I've tried cleaning the inner source, and reconditioning the column, and yet, I ran a blank (just Helium) and those 2 peaks remain. I wonder if anyone has experienced this before. Also... has anyone used the Clarus 500GC background substraction utility for the MS? According to the manuals, this utility allows the user to run a blank so a background file is recorded and automatically applied to further runs when using FID or any other detector for the GC standalone mode. The manual says it is possible to calibrate the background for MS (which I already did) "WHEN YOU SUBSECUENTLY TURN THE BACKGROUND COMPENSATION ON" (Clarus 500 GC Users Guide page 6-95), but when I ran a blank just after the calibration, the two "ghost" peaks still showed up in the chromatogram.

For applying the background recorded, I pressed "Run>>Start>>ok" as usual, and when "Waiting for injection" appeared in the PC screen; then I went to the GC touchscreen and went to "Tools>>Utilities>>Background Compen", selected "Method 5" (which is the one that assumes the PC method in my case), checked "apply calibration" and pressed "start run". I wonder if this procedure was correct, since i got the very exact same chromatogram for the background recording and for the ran blank.

Thank you very much for your comments

[Rndirk]

I am new to GC-MS and I would like to know how likely it is for multiple peaks to appear for a single mass.

I've tried cleaning the inner source, and reconditioning the column, and yet, I ran a blank (just Helium) and those 2 peaks remain. I wonder if anyone has experienced this before.

Yes. It is very likely for multiple peaks to appear in full scan GC-MS, even if you just inject solvent. Especially at low m/z (like 135). Septa of both the injection vial and the one that closes the injection port are a very common source of peaks. A fresh liner also shows peaks the first couple of runs.

My advice is to inject your standard solution in 2 different concentrations in full scan. Overlay it to see which peak shows a different area. In this way you can identify the retention time of your target component, and select ions from the full scan mass spectrum of this peak to put into a SIM method.

[Peter Apps]

You probably need to put in a clean inlet liner. This is a quick and cheap fix for a lot of carryover problems (i.e. peaks in blanks) that you should do before you do slow and difficult things like conditioning columns and cleaning MS ion sources.

Peter

[Francisco Franco]

I am new to GC-MS and I would like to know how likely it is for multiple peaks to appear for a single mass.

I've tried cleaning the inner source, and reconditioning the column, and yet, I ran a blank (just Helium) and those 2 peaks remain. I wonder if anyone has experienced this before.

Yes. It is very likely for multiple peaks to appear in full scan GC-MS, even if you just inject solvent. Especially at low m/z (like 135). Septa of both the injection vial and the one that closes the injection port are a very common source of peaks. A fresh liner also shows peaks the first couple of runs.

My advice is to inject your standard solution in 2 different concentrations in full scan. Overlay it to see which peak shows a different area. In this way you can identify the retention time of your target component, and select ions from the full scan mass spectrum of this peak to put into a SIM method.

Thank you very much for the clarification. I actually ran the standard because I ran an essential oil sample for a first glance on its contents, and when I found a method which gave good peak resolution I wanted to perform lib search... but before I even tried searching, I ran the standard and found more than one peak. So I am thinking of dealing with it by adjusting the lib search parameters, so peaks with similar areas to those of the peaks appearing at the standard solution are not taken into account in the integration step (I'm open to comments).

Have a great day

[Francisco Franco]

You probably need to put in a clean inlet liner. This is a quick and cheap fix for a lot of carryover problems (i.e. peaks in blanks) that you should do before you do slow and difficult things like conditioning columns and cleaning MS ion sources.

Peter

Thanks a lot for the advice. I forgot to mention that I cleaned the liner by sonicating it in methanol during 10 minutes when I was cleaning the inner source too (in different beakers).

[Peter Apps]

Thymol has a nice strong base peak at m/z 135, but that does not mean that a peak at m/z 135 necessarily comes from thymol. Do a library search on both, and a visual check of the spectra - one of them may not be thymol.

Peter