A gas-phase environment allows investigation of “unperturbed”, ie, solvent-free, structures of peptides. Although these structures may not be equivalent to those in the biological environment, the main features, which are controlled by the sequence of the peptide, may be similar in both cases. Tandem mass spectrometry (MS/MS) provides a method for the investigation of peptide structure, 18 including peptide conformation, 115 in the gas phase. The new MS/MS approach used here combines electrospray ionization (ESI)* 12 34with surface-induced dissociation (SID) 3-6 to determine fragmentation efficiency curves, which are shown to depend on the amino acid sequence of peptides. The curves are obtained by producing the protonated molecules of interest with ESI, colliding the selected MH+ ions into a surface, and recording the SID spectra. Fragmentation efficiency curves are a measure of how easily a peptide fragments and are obtained by plotting frag-mentation data acquired at a number of different collision energies, with a correction factor for peptide mass[E (fragment ion intensity)/E (total ion intensity) vs (collision energy)/(degree of freedom (DOF)) ratio7]. The sequence dependence of these curves can be combined with information on the specific fragment ions formed and with our previous quantum chemical calculations5 67* to predict the relative energy necessary to promote proton transfer and subsequent fragmentation of protonated peptides as a function of sequence.

In Figure 1, fragmentation efficiency curves are illustrated which were chosen to represent peptides with no basic residues, with a basic residue at the carboxy (C) terminus, and with a basic residue at the amino (N) terminus. Hereafter, basic residues will be indicated by the appropriate single letter code in boldface