A recently constructed miniature mass spectrometer, based on a cylindrical ion trap (CIT) mass analyzer, is used to perform ion/molecule reactions in order to improve selectivity for in situ analysis of explosives and chemical warfare agent simulants. Six different reactions are explored, including several of the Eberlin reaction type (M. N. Eberlin and R. G. Cooks, Org. Mass Spectrom., 1993, 28, 679-687) as well as novel gas-phase Meerwein reactions. The reactions include (1) Eberlin transacetalization of the benzoyl, 2,2-dimethyloximinium, and 2,2-dimethylthiooximinium cations with 2,2-dimethyl-1,3-dioxolane to form 2-phenyl-1,3-dioxolanylium cations, 2,2-dimethylamine-1,3-dioxolanylium cations and the 2,2-dimethylamin-1,3-oxathiolanylium cations, respectively; (2) Eberlin reaction of the phosphonium ion CH3P(O)OCH3+, formed from the chemical warfare agent simulant dimethyl methylphosphonate (DMMP), with 1,4-dioxane to yield the 1,3,2-dioxaphospholanium ion, a new characteristic reaction for phosphate ester detection; (3) the novel Meerwein reaction of the ion CH3P(O)OCH3+ with propylene sulfide forming 1,3,2-oxathionylphospholanium ion; (4) the Meerwein reaction of the benzoyl cation with propylene oxide and propylene sulfide to form 4-methyl-2-phenyl-1,3-dioxolane and its thio analog, respectively; (5) ketalization of the benzoyl cation with ethylene glycol to form the 2-phenyl-1,3-dioxolanylium cation; (6) addition/NO2 elimination involving benzonitrile radical cation in reaction with nitrobenzene to form an arylated nitrile, a diagnostic reaction for explosives detection and (7) simple methanol addition to the C7H7+ ion, formed by NO2 loss from the molecular ion of p-nitrotoluene to form an intact adduct. Evidence is provided that these reactions occur to give the products described and their potential analytical utility is discussed.