Proteins with a molecular mass in the range from approximately 5 to 100 kilodaltons are structurally analyzed without prior enzymatic digestion to small peptides in a mass spectrometer that operates with an ion trap. The proteins are ionized by electrospraying or similar processes to create highly charged analyte ions, which are then introduced into the ion trap and subjected to fragmentation and partial deprotonation in either order. The fragmentation may be ergodic or electron-induced. The result remaining in the ion trap is an evenly distributed mixture of fragment ions having between one and n charges, where n is a number between three and about eight. A mass spectrum is recorded from this mixture of fragment ions, which spectrum demonstrates a sequence coverage that far exceeds the mass range of the mass analyzer for singly charged ions.