Looking to use alternative carrier gas from Helium


I am putting together a proposal for the owner of the company I work for to make flavors. I cannot purchase the GC/MS system until I can determine if I can use an alternative carrier gas with good resolution,selectivity, etc. We are looking at buying 7890A GC with a 5975C msd as a detector. In the past at another company I used same equipment with helium as a carrier gas and built a mass spec library including retention times, etc. Using the column - DB-5ms 40m x 0.18mm x 0.18um. Now that Helium is difficult to get, when we buy this equipment from Agilent I want to start off using a carrier gas that is in constant supply. I understand I will have to update retention times for thousands of peaks so I need to know what you guys think I should use as a carrier gas other than helium. Should I not use Nitrogen? I remember reading in the Agilent class books from classes I took a few years ago that nitrogen will give some overlapping peaks at some point in the column depending on phase.Is it still not a good alternative to helium now that we may not be able to get helium at times. Is hydrogen ok to use with mass spec using a hydrogen generator? Could I use a combination of two gases?


Also, is there a newer method translation software so I could translate the old method and column to using a new type of column and carrier gas that may keep retention times somewhat close to original method. If I have to start over on the retention times then that is fine.

Thank you,

Dan Lingo

  • Hi danlingo,

    You may want to check this thread. It has links to calculators and a hydrogen reference package.




    As far as using N2, I have had a couple of customers try, its not a supported carrier gas for GCMSD. Mass 28 does not aid in creating an efficient mean free path in the MSD.




  • Hydrogen should be fine, but with a couple of issues. It is harder to pump down to high vacuum, but you are using a 0.18 ID column which only needs about half the amount of carrier gas amount for the same results as a 0.25 column. H2 is potentially reactive with some analytes in a hot injector; but assuming that you are using split injection that would be less of a problem, as you would be injecting a larger amount of analyte, so it is less likely to be degraded. Low level splitless injections could be more of a problem. H2 can give slightly different mass spectra than He, so Library searches may not be as reliable, but I have not found that to be much of a problem. H2 is a more efficient carrier gas (Look at Van Deemter curves for He, H2 and N2) so you can get better separations in the same time for H2 compared with He, or shorter analysis times for the same resolution.


    Hydrogen generators do have a number of advantages: they only generate relatively small amounts of hydrogen, so if you have a leak, they are much safer than a large cylinder; and they can generate hydrogen as pure as 99.99999% so you don’t need filters/purifiers in the gas line. However, the cost of ownership can be higher than using high purity H2 cylinders and purifiers.


    If your instrument uses another carrier gas as well as hydrogen the instrument background can be very high for several days as hydrogen "strips" previous contamination from surfaces. I agree with James' post, N2 is not a good choice.




  • Do you have to use a MS detector? If you could use a different detector then perhaps N2 is an option? I'm just remembering some old lab horror stories of GC's blowing up due to H2 leaks, although perhaps safety issues have been addressed in current systems. I've never had a problem ordering He cylinders. Perhaps an alternative is to always stock a minimum number of He cylinders to guard against temporary back order situations. (FYI, I'm in KS, USA, which may or may not effect my He availability.)

  • Nitrogen is not a very good GC carrier gas and is really poor inside the MS.  The only real alternative is hydrogen - but it has it's own set of issues as it is a very active chemical.   Hydrogen safety has been an Agilent concern forever and the GCs, Single Quad GCMS, and Tandem Quad GCMS systems are all tested for use with hydrogen (the QTOF cannot be used with hydrogen).   I just uploaded to this community the latest document with details about converting an Agilent GCMS system from Helium to Hydrogen. 

  • I will add a comment to Tim's post here. I would recommend gas trap especially with a H2 generator. I have had many issues through the years with H2 generators adding water and other impurity's to the background. Gas traps are cheap insurance against replacing an EPC module or two



  • HI,

    Thank you all for replying and adding your input. It has all been helpful. I think I will stick with using He.


    Could you guys give me a rough estimate on how long a 200 sq ft Helium tank lasts if it is in gas saver mode when not in use and if running 5~25 samples a day on a 0.18 ID column or similar? At first. I will be running the gc ms all day. I don't recall how long the tanks lasted when I used to run gc/msd setup. It seemed like sometimes we would go through a tank every 2mo. Also, what grade of helium do you use from say Airgas? I remember I need to use 99.9995%min purity but not sure if UPC grade is ok for running flavor raw materials. I could not find a purity for UPC grade listed.

  • A GCMS system is typically left running all the time as it takes some hours to pump down and achieve good vacuum and thermal stability.   A 0.18 mmid column will typically be used at a column flow rate of ~0.75 ml/min or so.  The GC Inlet should be run with Gas Saver ON at 20 ml/min after 2 minutes -- the default Gas Saver parameters. A 244 ft^3 helium tank is 6909 liters, but it's not a good idea to run the tank dry, so let's use a round number of 6500 liters.  6500 liters at 20 ml/min is something like 225 days.   Use an electronic leak checker on every connection outside of the GCMS !


    The site preparation document says 99.9995% or better helium.  Even if you are running a raw material, high concentration sample, you do not want to contaminate the GC inlet subsystem, the column, the MS ion source, and the entire MS vacuum chamber with low grade gas.  Any problems caused by contaminated gas are not covered by warranty nor service contracts.  Use high quality gas with high quality gas filters, like the GasClean filter, to keep your system clean.


    Another setting that will save you troubles....

    I recommend making a Standby.M method.  Have the inlet and transferline temperatures the same as you use in your run method. Have the source and quad temperatures in the tune file the same as your run method.  Have the oven temperature set above 75 degrees - I like 111 as I can read that from across the room.  If you are using the original brass column nut on the MSD transferline with a low standby oven temperature, the differential expansion of the brass to the MSD will sometimes lead to a leak there.  Leave the oven hotter than 75 all the time and this won't be a problem.  The fingertight nut for the transferline will help avoid any leaks there, too.

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