Chemical Ionization Reagent Selection and Manifold Construction

Return to Home Page

PowerPoint Presentation

This post includes information on the choice of amines as chemical ionization (CI) reagent gases and comparison of their relative sensitivity to methane and isobutane.  In addition, information is included for the instruction of a versatile CI manifold for multiple gases and gas mixtures needed to perform the experiments.

Liquid Reagents:  More recent work describes the substitution of liquids using Solvent Mediated Chemical Ionization (SMCI).  Lecture bottles of gasses can be difficult to purchase, somewhat hazardous to use, and even more difficult to dispose of when spent.  Thus the use of liquids for CI reagent gasses can offer some advantages using a novel manifold assembled out of spare parts.

Gas Reagents:  We offer a lots of tips on using gasses which is found in a copy of the prepress manuscript of a paper that we published in the Journal of the American Society for Mass Spectrometry in 2013.  The article was entitled "Qualitative Gas Chromatography-Mass Spectrometry Analyses Using Amines as Chemical Ionization Reagent Gases," by Adam S. Howard and James L. Little (; DOI:  10.1007/s13361-013-0740-8).

JASMS Article

We also published [see reference 1 below] a chapter in a book on "Deuterated Ammonia CHemical Ionization:  Using in Counting Exchangeable Hydrogen Sites on Organic Compunds."  Here is a copy of the unofficial version which has been modified with some additional information.

Encylopedia of MS Deuterium Exchange Article

Ammonia is normally adequate for most of our needs, but a mixture of methylamine in methane is very effective for determining the molecular weights of more labile compounds that extensively fragment with ammonia, isobutane, and methane.  In addition, the methylamine/methane mixture is very useful for resolving ambiguous ammonia CI data.

We also use deuterated ammonia to distinguish isomeric compounds and to confirm structures of unknowns.  Deuterated  methylamine and dimethylamine CI reagent gases can conveniently be prepared dynamically in the custom manifold described from a mixture of the appropriate alkylamine with deuterated ammonia.

Below is a picture of the current interface which is utilized on our Thermo DSQ GC-MS.  The picture below shows the manifold sitting to the left side of the GC-MS:


Similar information concerning the original manifold and its use for deuterium exchange work can be found in the chemical literature [1,2] and in the supplemental material included with the copy of the prepress manuscript of the Journal of the American Society for Mass Spectrometry article.

Agilent also offers many different application notes on CI GC-MS for their instrumentation on the internet [2-6].


1.  “Deuterated Ammonia Chemical Ionization: Use in Counting Exchangeable Hydrogen Sites on Organic Compounds,” A. Z Kamzelski, J. L. Little, The Encyclopedia of Mass Spectrometry, Volume 4, Fundamentals of and Applications to Organic (and Organometallic) Compounds, Edited by M Gross et al, p 772-780, D. M Parees, 2005.
2.  "Counting Exchangeable Protons in Organic Compounds Using Deutereated Amine Chemical Ionization," J. Little, D. Parees, A. Kamzelski, preprint of published article with additional references, Dec. 2014.
3.  Agilent Application Notes on Chemical Ionization, PDF containing References 4-7 Below Combined.
4.  Prest, H., Thomson, C., Arnold, K., Sanderson, R.:  Implementation of  ammonia reagent gas for chemical ionization of 5973 MSDs, Agilent Technologies, 5968-7844E (2000).
5.  Agilent Technologies: Using other reagent gases for CI operation applies to 5973A/N MSD, Agilent Technologies, A20749.doc.
6.  Thomson, C., Foote, J., Peterson, D., Prest, H.:  Implementation of ammonia reagent gas for chemical ionization on the 5975 series MSDs,  Application Note 5989-5170EN,  Agilent Technologies (2006).
7.  Sandy, C., Garnier, J., Prest, H.:  The 5975 inert MSD-benefits of enhancements in chemical ionization operation, Agilent Technologies Technical Note 5989-4347EN (2005).

Return to Home Page

Scroll to Top