For characterization of sequence and posttranslational modifications, molecular and fragment ion mass data from ionizing and dissociating a protein in the mass spectrometer are far more specific than masses of peptides from the protein's digestion. We now extend the ~500 residue, ~50 kilodaltons (kD) dissociation limitation of this top-down methodology by using electrospray additives, heated vaporization, and separate noncovalent and covalent bond dissociation. This process can cleave 287 interresidue bonds in the termini of a 1314 residue (144 kD) protein, specify previously unidentified disulfide bonds between 8 of 27 cysteines in a 1714 residue (200 kD) protein, and correct sequence predictions in two proteins, one with 2153 residues (229 kD).