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RATIONALE Ammonia (NH3) is an important chemical target in sensor applications such as trace explosives detection of ammonium nitrate (NH4NO3) and environmental monitoring. Ion-molecule reagent chemistries show potential to increase sensitivity in detection systems relying on atmospheric pressure ionization (API) of reagent-ammonium (M + NH4+) complexes. Gas-phase reagent selection assessment is based on mass spectrometric (MS) determination of binding constants relative to competitive ions and critical energies for ion-molecule complex dissociation. METHODS Eight ammonium complexation reagents were identified and gas-phase ion-molecule interactions were studied using electrospray ionization. Binding constants were determined, in Log(K), using the competition method for one host molecule with three guests (NH4+, Na+, and K+) in single quadrupole MS. Critical energy determination was based on calibration of threshold activation voltage using collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). RESULTS This assessment informs selective binding affinity and intrinsic ion-molecule critical energy for dissociation. Relative NH4+ binding affinity was highest for sucrose and 4-tert-butylcalix[6]arene, while 4-tert-butylcalix[6]arene and methyl acetoacetate showed the highest preferential binding of NH4+ versus Na+ and K+. The intrinsic critical energy for NH4+ binding was highest for crown ethers, tetraglyme and methyl acetoacetate. CONCLUSIONS An MS-based framework was developed to quantitatively assess API ion-molecule reagent chemistries based on ammonium selectivity versus competing ions, and intrinsic ammonium binding strength and complex survivability for detection. Methyl acetoacetate is an attractive ammonium reagent for vapor-phase API techniques given its high vapor pressure, preferential selectivity, and high critical energy for dissociation. Copyright © 2013 John Wiley & Sons, Ltd.