GCMS using H2 carrier

The high background may persist for a while, maybe a long while, depending on the cleanliness of the gas tank regulator or hydrogen generator, tubing, fittings, traps, etc. A long while could be more than ten days.... 

EI GC/MS Instrument Helium to Hydrogen Carrier Gas Conversion User Guide (agilent.com)

It's not useful to just bake the source to get rid of any contamination that shows up due to hydrogen. Agilent sells JetClean - which puts a very small amount of hydrogen into the MS which, along with an operating filament, scrubs the ion source.  Your system is running hydrogen carrier and essentially doing higher flow JetClean - so it's best to run the filament to create the same environment inside the ion source that is used during JetClean operation to clean it.  

There will be a reduction in sensitivity compared to using a GCMS running Helium. This is due to the physics and chemistry involved inside the ion source and not ion source or system design. Hydrogen is fine to use in an Agilent GCMS, but it is not a direct replacement for Helium.

Do you have the recommended 9mm Draw Out/Extractor lens installed?

Hi.  I have the 6mm draw out which was recommended.  I had thought there was only a 3mm and a 6mm, didn't realize there was a 9mm as well.  I am in the middle of a source condition recommended in the user guide you referenced.  The background counts are continuously dropping so I am hoping this helps some.  I've been running samples on the instrument only 2 days now so I might have to be more patient as you said it could take longer.

Make sure to lower your column flow compared to running helium.  

If on Helium your application is typically around 1.2 ml/min, on Hydrogen it should be approximately 1/2 of that -- like 0.6 to 0.7 ml/min.  The guide suggests a smaller ID column, with it's required lower sample loading, to help keep the inlet pressure high enough for decent column head pressure, and therefore column flow, control 

Changing to hydrogen is a dance with many partners...

Thank you.  My H2 flow is set at 0.5mL/min right now.  I have the recommended column for H2 as well.  I will give it more time and hopefully find the right dance partner!  :-)

Post back here if you have further questions!

Post back here if you have further questions!

Hi Paul.  I am going to attach a chromatogram here.  You will see that especially after all the peaks the background/tailing is high.  I don't see this on my other instruments.  You were right, the source conditioning did nothing for the background.  :-)  I am using etune which changes the repeller voltage from 34 to 3 and also sets an extractor lens voltage with it.  When I use atune, repeller is 34, extractor is 0 and there is no tailing/little background but the counts are much lower.  Would you always recommend the etune when you have a system with the extractor source?  Or can either be used?  I want to make full use of my new source and would prefer etune.  Also, with the larger diameter draw outs, I am guessing it lets more ions through so more counts but decreases resolution/increases tailing?

fentanyl test.TIF

The extractor source makes more ions - is more sensitive. Etune drives the system to take advantage of the design.  This happens as the repeller is pushing and the extractor is pulling - at least that's how I explain it. Either tune can be used, you just have to understand the pluses and minuses.

The larger hole in the Draw Out/Extractor lens reduces the ionization volume 'pressure'  -- it lets molecules and ions out faster than the smaller holes.  This is important with the many more hydrogen molecules for the same flow than you'd have with hydrogen.  The effect is that it raises the linear range to a higher level.  It does not increase the dynamic range, it gives up some ultimate low end sensitivity to gain higher concentration linearity.

Tailing very, very rarely happens in the source. It is essentially always in the inlet.  I'd have to play with the data file in MassHunter Qual to know for sure, but the little 4.892 and 6.249 peaks are not tailing.   What GC, inlet, inlet injection mode and parameters, liner, injection volume, column, column installed height...all those little things?   

We can go back and forth here if you'd like, but it may be better if you called Agilent and spoke to the Online Technical Support folks who know about applications.  Fentanyl is a tough compound to chromatograph anyway.  How does it look with a boring simple easy non-reactive sample?

Thank you for all your help.