The scope of this thesis is the electronically excited state dynamics of protonated peptides and their photofragmentation mechanism. UV radiation induces fragmentation of biological molecules and might cause various diseases, such as cataracts or skin cancer. The transition to the electronically excited states is the first step in the complex chain of photochemical reactions that lead to UV-induced photodamage. By performing experiments in the gas phase, one can separate the intrinsic photophysical properties of peptides from those involving solvent, potentially yielding insight into both. The main part of this work presents evidence that following near-UV excitation of tyrosine or phenylalanine residues in gas-phase protonated peptides, some fraction of the molecules undergoes intersystem crossing to the triplet state. This pathway competes with direct dissociation from the excited electronic state and with dissociation from the electronic ground state subsequent to internal conversion. We employ UV-IR double-resonance photofragment spectroscopy to record conformer-specific vibrational spectra of cold peptides pre-excited to their S1 electronic state. The absorption of tunable IR light by these electronically excited peptides leads to a drastic increase in fragmentation, selectively enhancing the loss of neutral phenylalanine or tyrosine side-chain. The recorded IR spectra evolve upon increasing the time delay between the UV and IR pulses, reflecting the dynamics of the intersystem crossing on a timescale of ~80 ns and <10 ns for phenylalanine- and tyrosine-containing peptides respectively. The IR spectra in 6 micron region reveal the absence of proton transfer during this time. Once in the triplet states, phenylalanine-containing peptides may live for more than 100 ms, unless they absorb IR photons and undergo dissociation by the loss of an aromatic side-chain. We discuss the mechanism of this fragmentation channel and its possible implications for photofragment spectroscopy and peptide photostability. The second part describes conformer-dependent anharmonic coupling between fast and slow vibrations in an electronically excited protonated tri-peptide. By analyzing the infrared spectra of different vibrational levels of the S1 electronic state and performing DFT calculations, we identify the vibrational modes involved in the coupling, the nature of this coupling, and which conformational changes induce it. The last part presents the combination of cold ion spectroscopy, 13C isotopic labeling, and DFT calculations to determine coupling between different amide chromophores in a helical peptide. These results are used to assess the spectroscopic maps developed for protein structure elucidation in solution.