Chromatography Forum

I am trying to determine the cause of the following problem. I am learning to operate, interpret, and repair an Agilent 5973N Mass Spec (EI) on my own. Any advice will be greatly appreciated.


After source cleaning and EM horn replacement, the 5973N mass spec appeared to work. A solution of C9-C10-C11 straight chain alcohols in n-hexanes gave three peaks with correct mass spectra appearance and library identification for 2 out of 3 peaks.


Now, the Mass Spec (EI) lost sensitivity overall, especially for the lower molecular weight compound. Mass Spectra now do not look like the known library spectra. But, the autotune looks better than it has in months.

When the sample is acetylated, all 3 alcohols are observed with slightly shifted retention times.


Chromatograms with overlay and autotune are attached.


Again, any advice will be greatly appreciated for this novice GC-MS user.

Hello

It looks like nothing is reaching MS detector (or very small amount).
I'd check:
1.GC - Sampler (syringe/plunger/leak), column (if it is properly installed in inlet), inlet (leak, liner)
2.Is the column properly installed from MS side? It should be about 1-2mm from transfer line to analyzer (ion source).

Regards

Tomasz Kubowicz

I would agree with Tomasz. If tune says MS is working then I would say it's the GC (or other sample introduction to the MS).

I have had, in one rare occurrence, a case where a data file was corrupted and opened fine but showed an entirely different chromatogram/spectra. This was an identical copied file that 3 of us grad students were using for a TAing a lab and opened on three identical copies of MSD Chemstation. Solution was to re-copy the data file again and it looked fine then.

If all acquisition methods and parameters are the same as before and the problem can be duplicated, then it is most definitely sample introduction.