Chromatography Forum

Dear All,
I am working on analysis of a compound which is having the chlorine in the molecule and also having dichloro impurity. (Molecular mass is more than 150 and boiling point is more than 20
when i am doing GC MS on EI mode of that sample i am not getting the Molecular ion peak properly (the intensities of that is less than o.1% of the base peak.)
i am bit surprise as in EI mode i saw this trend 1st time.
I know for molecular ion peak CI mode is more suitable as this one is soft ionization as compared to EI which is an hard ionization.
I dont have the CI mode currently so i tried it to increase the molecular ion peak by changing the Voltage from 70 Ev to varies up to 15EV but not getting success.
If anyone can help me to get the knowledge why this is happening and with the available EI source how i can get molecular ion peak atleast 5-10% of base peak.
Even the same work we did with bromine also instead of chlorine and in that also we have found the same results.
Now i need to understand why this is happened and what more we can do (Other than Volatge variation) to get the molecular ion peak up to some extent.
this will help us to get confidence over other impurities also which is available in the samples.

Normally you should see at least some molecular ion even if it's not super prominent, but for big complicated molecules you can still get very little molecular ion.

Although lowering ionization energy does tend to decrease fragmentation, it also dramatically lowers ionization efficiency so you can end up decreasing your signal quite a bit also. As it so happens, 70EV is used because it's something of a sweet spot of ionization efficiency(which isn't great in EI anyway-techniques like ESI and APCI are orders of magnitude better in this respect, which is part of the reason why LC-MS gets a lot of attention for trace detection, but that's another topic).

What I might try is lowering the filament current while leaving it at 70EV. This tends to decrease fragmentation also.

Also, what brand and model of GC-MS are you using? If you really want to do CI, sometimes it's possible to at least get it functional. The manufacturers don't officially support it generally, but it can sometimes be done. On Agilent instruments, I've sort of done it on a 5971(upgraded to 5972 electronics) in a way that James Ball(member here) suggested-basically I fitted a CI source(you can buy one from Agilent for the 5973-75-77-I was given one for a 5971/72) and used a T fitting on the end of the transfer line and used a Restek deactivated guard column to feed methane from a second inlet at a very low flow rate. I later got my hands on a proper 5971/72 CI manifold, which actually works a lot like this. CI on that instrument doesn't work great, but it did give me M+1 molecular ions reliably if I had enough sample.

What is the carrier gas? Is it hydrogen?

If it is hydrogen, I would recommend helium, at least until you can troubleshoot the ionization problem. Hydrogen is a known problem with chlorinated compounds, but sometimes these problems can be overcome with an inert source if you choose to use hydrogen. Start with helium to keep it simple.

Lowering the filament current a small amount is a good idea to try. Lowering the EI voltage isn't likely to help too much, especially below 20 eV, it becomes fruitless. You may be able to lower the source temp. a little if you believe the problem is source chemical reactivity.