Proteo-SAFARI also includes an interactive annotated spectrum visualization within the application, enabling an easy-to-use platform with which to manually analyze identified fragments. 10+, 12+, and 14+ precursor charge states. Previous examination of supercharged proteins characterized using 193 nm UVPD revealed prevalent preferential backbone cleavages N-terminal to proline residues, resulting in elevated abundances of certain y ions. Interestingly, these fragment ions exhibit a gradual but notable change in the pattern of hydrogen migrations, observed for these y ions as hydrogen losses yielding y-1 and y-2 ions. For the more standard charge states of ubiquitin (8+ and 10+ in Figure ), the y58 ions generated by UVPD are predominantly composed of y58-2 ions based on the calculated nonnegative least squares fit, while the analogous y58 ions generated by HCD exhibit no hydrogen losses. For supercharged states (12+ and 14+ in Figure ), the prevalence of the hydrogen shifts decreases for the y58 ions produced by UVPD, and again HCD results in no notable hydrogen shifts. The mechanism of this hydrogen shift process that accompanies protein fragmentation during UVPD is not fully resolved but may signal a transition from direct bond cleavage of an ion in an excited state to a fragmentation process occurring after internal conversion and intramolecular vibrational energy redistribution (the latter being the more CID-like route). The presence of additional mobile protons in the supercharged proteins may modulate this process. For this example, Proteo-SAFARI facilitated confident confirmation of the prevalence of the hydrogen shifts in specific fragment ions. Proteo-SAFARI can also annotate fragment ions in complex MS/MS spectra of larger proteins, as demonstrated for EThcD of enolase (52+) in Figure with a corresponding sequence coverage map in Figure . After EThcD, the fragment ion populations in the m/z regions lower and higher than the precursor ion were isolated and subjected to PTCR. PTCR dispersed the fragment ions over a broader m/z range, alleviating overlapping isotope distributions of fragment ions and facilitating their confident assignment. These spectra, recorded in full profile mode, were annotated by Proteo-SAFARI, resulting in 65% sequence coverage of this 46.8 kDa protein.