Evidence for ionization-related conformational differences of peptide ions in a quadrupole ion trap.

The differences in boundary-activated dissociation (BAD) onsets have been investigated for peptide ions that were generated by two different ionization techniques, nanoflow electrospray ionization (nanoESI) and liquid secondary-ion mass spectrometry (LSIMS). BAD onsets of these ions were determined to compare the relative internal energies of the ions. Protonated peptide ions formed by nanoESI had lower BAD onsets than ions formed by LSIMS. The BAD onsets of peptides derivatized to have a fixed charge on the N-terminus also were lower for those generated by nanoESI than those generated by LSIMS. The BAD onsets of ions formed by nanoESI did not change with the variation of collisional cooling periods after gating ions into the ion trap and after isolating them prior to dissociation, indicating that the ions formed by the two ionization techniques would not adopt the same energy distributions. It is proposed that the ions formed by the two techniques differ in secondary structure, and the LSIMS ions are collisionally cooled to a lower local minimum along the potential energy surface than the nan