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The impact of supercharging on the fragmentation patterns of six proteins, ubiquitin, cytochrome c, staph nuclease, myoglobin, dihydrofolate reductase, and carbonic anhydrase, was investigated for five activation methods, HCD, ETD, EThcD, 213 nm UVPD, and 193 nm UVPD under denaturing conditions. Changes in sequence coverage, alterations in the number and abundance of preferential cleavages (N-terminal to proline, C-terminal to aspartic or glutamic acid, adjacent to aromatic residues), and changes in individual fragment ion abundances were evaluated. Large decreases in sequence coverage were observed upon supercharging of proteins activated by HCD, whereas modest gains were observed for ETD.

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