The mechanism of the cleavage of protonated amide bonds of oligopeptides is discussed in detail exploring the major energetic, kinetic, and entropy factors that determine the accessibility of the bx-yz (Paizs, B.; Suhai, S. Rapid Commun. Mass Spectrom.2002,16, 375) and “diketopiperazine” (Cordero, M. M.; Houser, J. J.; Wesdemiotis, C. Anal. Chem.1993,65, 1594) pathways. General considerations indicate that under low-energy collision conditions the majority of the sequence ions of protonated oligopeptides are formed on the bx-yz pathways which are energetically, kinetically, and entropically accessible. This is due to the facts that (1) the corresponding reactive configurations (amide N protonated species) can easily be formed during ion excitation, (2) most of the protonated nitrogens are stabilized by nearby amide oxygens making the spatial arrangement of the two amide bonds (the protonated and its N-terminal neighbor) involved in oxazolone formation entropically favored. On the other hand, formation of y ions on the diketopiperazine pathways is either kinetically or energetically or entropically controlled. The energetic control is due to the significant ring strain of small cyclic peptides that are co-formed with y ions (truncated protonated peptides) similar in size to the original peptide. The entropy control precludes formation of y ions much smaller than the original peptide since the attacking N-terminal amino group can rarely get close to the protonated amide bond buried by amide oxygens. Modeling the bx-yz pathways of protonated pentaalanine leads for the first time to semi-quantitative understanding of the tandem mass spectra of a protonated oligopeptide. Both the amide nitrogen protonated structures (reactive configurations for the amide bond cleavage) and the corresponding bx-yz transition structures are energetically more favored if protonation occurs closer to the C-terminus, e.g., considering these points the Ala(4)-Ala(5) amide bond is more favored than Ala(3)-Ala(4), and Ala(3)-Ala(4) is more favored than Ala(2)-Ala(3). This fact explains the increasing ion abundances observed for the b2/y3, b3/y2, and b4/y1 ion pairs in the metastable ion and low-energy collision induced mass spectra (Yalcin, T.; Csizmadia, I. G.; Peterson, M. B.; Harrison, A. G. J. Am. Soc. Mass Spectrom.1996,7, 233) of protonated pentaalanine. A linear free-energy relationship is used to approximate the ratio of the bx and yz ions on the particular bx-yz pathways. Applying the necessary proton affinities such considerations satisfactorily explain for example dominance of the b4 ion over y1 and the similar b3 and y2 ion intensities observed for the metastable ion and low-energy collision induced mass spectra.