n-paraffin fragmentation issues Saturn 2100T Ion Trap MS

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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I am attempting some hydrocarbon runs on a Saturn 2100T Ion Trap MS. The sample is from a catalysis process called Fischer-Tropsch, which mainly produces 4 major components per carbon number that elute in this order; 1-olefin, n- paraffin, trans-2-olefin, cis-2-olefin.
I'd like to specifically look at the parent ion because of some C13 work, but I am not able to see it. The picture is a scan of C11 (n-paraffin), and even if I zoom in, the parent ion is not there.

The three large peaks are 57, 71, 85 m/z. I can provide a bigger picture if necessary.

I have tuned the MS, baked the column (though it is a bit older), cleaned the inlet (with new septa) and played with the scanning of the trap - (used EI Auto, shortened the scan time and pre-scan time, dropped the emission current to 5). Nothing has helped. I still get the fragmentation pattern seen in the picture. Further, it does not seem to matter which n-paraffin I look at, they are essentially the same.

It seems as if I am getting some unnecessary fragmentation due to a dirty source or the column just bleeding too much. I understand that CI would be a good option as well, but before I go off and switch all this around I wanted to see the opinion of others. I mainly have worked with Agilent GCMS with quads, not traps.

N-paraffins do not exhibit molecular ions in ion traps MS due to undesirable MS-MS in the ion extraction path into the ion detector. Thus, you get what you should get and your system is OK.
In quadrupole MS hydrocarbons are exhibiting molecular ions with relative abundance that decline with the number of carbon atoms and can be observed up to about C24. Above this and for branched hydrocarbons you may need Cold EI. For more details you may write me at amirav@tau.ac.il
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