Chemical ionization (CI) remains one of the most valuable techniques for determining the molecular weights of compounds that produce weak or absent molecular ions by electron ionization (EI). The choice of reagent gas can dramatically influence sensitivity, fragmentation, and the quality of molecular weight information obtained.

This page brings together our publications, practical experience, and construction details for a versatile CI manifold that allows rapid switching between multiple reagent gases and dynamic preparation of gas mixtures. It also includes our work on deuterium exchange and newer solvent-mediated chemical ionization (SMCI) techniques that use liquid reagents.

Featured Resources

This page includes the following publications and supplementary material:

• Journal of the American Society for Mass Spectrometry (2013)
  Qualitative Gas Chromatography-Mass Spectrometry Analyses Using Amines as Chemical Ionization Reagent Gases
  Adam S. Howard and James L. Little

  This paper compares ammonia, methylamine, dimethylamine, methane, and isobutane CI reagent gases, discusses their relative sensitivities, and provides extensive practical guidance for selecting reagent gases. The accompanying supplementary material includes detailed instructions for constructing and operating a versatile multi-gas CI manifold.

• Encyclopedia of Mass Spectrometry (2005)
  Deuterated Ammonia Chemical Ionization: Use in Counting Exchangeable Hydrogen Sites on Organic Compounds

  This chapter describes the use of deuterated ammonia CI to determine the number of exchangeable hydrogens in organic molecules, distinguish structural isomers, and aid in the identification of unknown compounds. An updated unofficial version with additional discussion is also provided.

• Solvent-Mediated Chemical Ionization (SMCI)

  More recent work demonstrates the use of liquid reagents, such as propylamine, as an alternative to traditional lecture bottles of reagent gases. Solvent-mediated CI simplifies reagent handling, reduces safety concerns, and eliminates many of the difficulties associated with purchasing and disposing of compressed gas cylinders.

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Selecting the Appropriate CI Reagent

For most routine GC-MS analyses, ammonia remains our preferred reagent gas because it:

• provides reliable molecular weight information
• produces acceptable sensitivity
• generates relatively little fragmentation
• is readily available
• does not cause carbon contamination within the ion source

However, some compounds fragment extensively under ammonia CI conditions.

In these cases, methylamine in methane is often a much better choice. This reagent mixture significantly reduces fragmentation while preserving excellent molecular weight information for thermally or chemically labile compounds. It is also extremely useful for resolving ambiguous ammonia CI spectra.

Dimethylamine mixtures can provide similar benefits, although methylamine generally offers a better balance of sensitivity and chemical background.

Deuterium Exchange Chemical Ionization

Deuterated ammonia CI is a powerful structural elucidation tool that complements conventional CI analyses.

Applications include:

• determining the number of exchangeable hydrogens
• distinguishing structural isomers
• confirming proposed molecular structures
• supporting unknown identification

Our custom manifold also allows deuterated methylamine and deuterated dimethylamine reagent gases to be prepared dynamically by mixing the appropriate alkylamine with deuterated ammonia. This provides an inexpensive and convenient alternative to purchasing specialty deuterated reagent gases.

Versatile Multi-Gas CI Manifold

The custom manifold described in our publications was developed to simplify switching among multiple CI reagent gases and to permit dynamic preparation of gas mixtures.

The design allows rapid selection of reagent gases while minimizing contamination from previous gases and provides convenient preparation of mixtures such as:

• methylamine in methane
• dimethylamine in methane
• deuterated methylamine
• deuterated dimethylamine

The photograph below shows the current manifold installed beside our Thermo DSQ GC-MS instrument.

Detailed construction drawings, parts lists, operating procedures, and practical troubleshooting tips are included in the supplementary material accompanying the JASMS publication.

Additional Resources

Several manufacturers provide excellent application notes on chemical ionization GC-MS. Agilent Technologies has published numerous guides covering ammonia CI operation, alternative reagent gases, and optimization of their GC-MS systems.

Agilent Information

In addition, JEOL has produced an excellent collection illustrating the differences between several soft ionization techniques, including:

• Chemical Ionization (CI)
• Electron Ionization (EI)
• Photoionization (PI)
• Field Ionization (FI)

These comparisons provide a useful overview of how different ionization methods affect molecular ion formation and fragmentation.

Others have noted that low eV (10-20 eV) and cold EI ionization can sometimes offer useful molecular weight information.  Apparently, newer source designs can overcome low sensitivity issues for low eV EI previously noted with this approach.

References

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.  Agilent Application Notes on Chemical Ionization, PDF containing References 4-7 Below Combined.
3.  Prest, H., Thomson, C., Arnold, K., Sanderson, R.:  Implementation of  ammonia reagent gas for chemical ionization of 5973 MSDs, Agilent Technologies, 5968-7844E (2000).
4.  Agilent Technologies: Using other reagent gases for CI operation applies to 5973A/N MSD, Agilent Technologies, A20749.doc.
5.  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).
6.  Sandy, C., Garnier, J., Prest, H.:  The 5975 inert MSD-benefits of enhancements in chemical ionization operation, Agilent Technologies Technical Note 5989-4347EN (2005).
7.  JEOL GC-MS SOft Ionization Mass Spectral Collection (EI, CI, PI, FD), pdf file

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