We gauged the internal energy transfer for two dissociative ion decomposition channels in matrix-assisted laser desorption ionization (MALDI) using the benzyltriphenylphosphonium (BTP) thermometer ion [PhCH2PPh3](+). Common MALDI matrixes [alpha-cyano-4-hydroxycinnamic acid (CHCA), 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid, SA), and 2,5-dihydroxycinnamic acid (DHB)] were studied with nitrogen laser (4 ns pulse length) and mode-locked 3 x omega Nd:YAG laser (22 ps pulse length) excitation. Despite the higher fluence required to initiate fragmentation, BTP ions indicated lower internal energy transfer with the picosecond laser in all three matrixes. These differences can be rationalized in terms of phase explosion induced by the nanosecond laser vs a stress-confinement-driven desorption mechanism for the picosecond laser. For the two ion production channels of the BTP thermometer ion, breaking a single bond can result in the formation of benzyl/tropylium ions, F1, or triphenylphosphine ions, F2. In SA and DHB, as well as in CHCA at low fluence levels, the efficiency of these channels (expressed by the branching ratio IF1/IF2) is moderately in favor of producing tropylium ions, 1 < IF1/IF2 < 6. As the laser fluence is increased, for CHCA, there is a dramatic shift in favor of the tropylium ion production, with IF1/IF2; 30 for the nanosecond and the picosecond laser, respectively. This change is correlated with the sudden increase in the BTP internal energies in CHCA in the same laser fluence range. The large changes observed in internal energy deposition for CHCA with laser fluence can account for its ability to induce fragmentation in peptides more readily than SA and DHB.