Ion mobility measurements have been performed for protonated polyalanine peptides (A(10) + H+, A(15) + H+, A(20) + H+, A(25) + H+, and A(15)NH(2) + H+) as a function of temperature using a new high-temperature drift tube. Peaks due to helices and globules were found at room temperature for all peptides, except for A(10) + H+ (where only the globule is present). As the temperature is increased, the helix and globule peaks broaden and merge to give a single narrow peak. This indicates that the two conformations interconvert rapidly at elevated temperatures. The positions of the merged peaks show that A(15) divided by H-divided by and A(15)NH(2) divided by H-divided by spend most of their time as globules when heated, while A(20) divided by H-divided by and A(25) divided by H-divided by spend most of their time as helices. The helix/globule transitions are almost certainly accompanied by intfamolecular proton transfer, and so, these results suggest that the proton becomes mobile (able to migrate alone the backbone) at around 450 K. The peptides dissociate as the temperature is increased futher to give predominantly the b(n)(+), b(n-1)(+), b(n-2)(+),... series of fragment ions. There is a correlation between the ease of fragmentation and the time spent in the helical conformation for the A(n) divided by H-divided by peptides. Helix formation promotes dissociation because it pools the proton at the C-terminus where it is required for dissociation to give the observed products. In addition to the helix and globule, an antiparallel helical dimer is observed for the larger peptides. The dimer can be collisionally dissociated by injection into the drift tube at elevated kinetic energies.