Samples of biomolecules with low vapor pressures, specifically α-amino acids, were introduced by a direct insertion probe into the ion source of a pulsed ionization high-pressure mass spectrometer. The number density of an amino acid in the source was determined by a new technique based on the measurement of the rate of its protonation by t-C4H9+, the chemical ionization reactant ion. The proton affinities (PA) of the amino acids were obtained from measurements of the thermodynamics of proton transfer equilibria between the amino acids and appropriate reference bases. The following PAs (referred to PA(NH3) = 202.3 kcal mol-1) were obtained : glycine (208.2), alanine (212.2), valine (213.9), leucine (214.5), phenylalanine (215.1), proline (218.4). Comparison with the proton affinities of alkylamines shows that substitution by a carboxyl group decreases the proton affinity of the amine function by 1.8-3.1 kcal mol-1. Comparison with solution basicities shows that the effect of solvent (H2O) on this substituent effect is minor, if any, On the basis of the measured PA values, the following gas-phase heats of formation (ΔH°f)g are determined : GlyH+ (53), AlaH+ (43), LeuH+ (15), and PheH+ (57). Comparison of (ΔH°f)g of the ion-molecule association products CH3NH3+•CO2 and C2H5NH3+•CO2 with (ΔH°f)g of their isomers GlyH+ and AlaH+ shows that the hydrogen-bonded cluster ions are more stable by 11 and 8 kcal mol-1, respectively, then their covalently bonded isomers. We also observed the formation of the hydrogen-bonded dimers (Gly)2H+ and (Pro)2H+. For the association reactions leading to these dimers we measured ΔH° = -31 and -29 ± 2 kcal mol-1 and ΔS° = -33 and -32 ± 5 cal mol-1K-1, respectively. © 1979, American Chemical Society. All rights reserved.