Tandem mass spectrometry of very large molecules. 2. Dissociation of multiply charged proline-containing proteins from electrospray ionization.

Collisional dissociation tandem mass spectra have been obtained for multiply charged molecules produced by electrospray ionization for a variety of proline-containing proteins extending up to 22,000 molecular weight. Interpretation of limited m/z range, low-resolution tandem mass spectra from multiply charged precursors can present difficulties due to the possibility of multiply charged product ions and the lack of unambiguous charge-state information. Methods used to guide the spectral interpretation process under these circumstances are discussed. Proline is a unique amino acid constituent because its side chain is bonded to the tertiary nitrogen in a cyclic pyrrolidine ring. For large polypeptides containing proline residues, we have observed that fragmentation due to cleavage of the amide bond to proline is often dominant. Such proline-directed processes are often the only dissociation pathways observed for large proteins. This is attributed to the quasithermal nature of large molecule collisional activation/dissociation processes and the lower dissociation energies for peptide bonds near proline residues. The present results also suggest possible effects on the dissociation processes for large molecules due to charge location and perhaps protein conformation.