Charge state distribution (CSD) and hydrogen/deuterium (H/D) exchange of preparations of alpha-lactalbumin (alpha-Lac) and beta-lactoglobulin (beta-Lg) were investigated using electrospray ionization mass spectrometry (ESI-MS). Storage of alpha-Lac at pH 3 resulted in substantial changes in its CSD, with the emergence of new ion species and shifts toward higher charge state, indicating less stable conformation. ESI spectra of alpha-Lac kept at pH 5.5 for 4 days showed stable conformation; however, extending the storage period resulted in substantial changes in CSD and a decrease in the stability of holo-alpha-Lac (Ca(2+)-bound form). In comparison to apo-alpha-Lac, the relative intensity of holo-alpha-Lac was higher at pH 6.8 but lower at pH 8 during the storage period. beta-Lg showed stable CSD at pH 3, substantial changes at pH 5.5, and minor changes at pH 6.8 and 8 during storage. The H/D exchange results demonstrate that the conformation of holo-alpha-Lac was more stable than that of apo-alpha-Lac and that the conformation of beta-Lg variant B was more stable than that of the beta-Lg variant A. Kinetics of H/D exchange indicated that alpha-Lac and beta-Lg fractions obtained from whey protein preparations have the same or improved conformational stabilities compared to those of alpha-Lac and beta-Lg standards. The presence of four or more hexose residues in alpha-Lac enhanced its conformational stability; the presence of two hexose residues in beta-Lg resulted in a less stable conformation.