We present a mass spectrometric method for analyzing protein structure and function, based on the imidazole C-2 or histidine C-e1 hydrogen/deuterium (HID) exchange reaction, which is intrinsically second-order with respect to the concentrations of the imidazolium cation and OD- in D2O. The second-order rate constant (k(2)) of this reaction was calculated from the pH dependency of the pseudo-first-order rate constant (k(phi)) obtained from the change in average mass [Delta M-r (0 < Delta M-r < 1)] of a peptide fragment containing a defined histidine residue at incubation time (t) such that K phi = -[1n(1 - Delta M-r)]/t. We preferred using k(2) rather than K phi, because k(2)(max) (maximal value of k(2)) was empirically related to pKa as illustrated with a Bronsted plot [log k(2)(max) = -0.7pK(a) + a (a is an arbitrary constant)], so that we could analyze the effect of structure on the HID exchange rate in terms of log(k(2)(max)/k(2)) representing the deviation of k(2) from k(2)(max). In the catalytic site of bovine ribonuclease A, His 12 showed a change in log(k(2)(max)/k(2)) much larger than that of His119 upon binding with cytidine 3'-monophosphate, as anticipated from the X-ray structures and the possible change in solvent accessibility. However, we need to consider the hydrogen bonds of the imidazole group with nondissociable groups to interpret an extremely slow HID exchange rate of His48 in a partially solvent-exposed situation.