Spatial extent of fragment-ion abundances in electron transfer dissociation and electron capture dissociation mass spectrometry of peptides

Abstract

Earlier work from the first author's group has suggested that, in electron capture dissociation (ECD) or electron transfer dissociation (ETD) mass spectrometry experiments, an electron is initially attached into a Rydberg orbital centered at one of the peptide's positive sites (likely a protonated N-terminus, Lysine, Arginine, or Histidine). Moreover, this earlier work predicted that only Rydberg orbitals having principal quantum numbers n=3–6 are populated in ECD and only n=3 and 4 in ETD (when an anion donor having an electron binding energy of ca. 0. 6eV is used), and that the populations of these levels are very similar in the nascent charge-reduced peptide. Based upon these predictions, the present paper develops a framework for predicting the abundances of closed-shell c and open-shell z fragments as a function of distance along the backbone from the site initially holding the attached electron in a Rydberg orbital. The framework is not aimed at differences in branching ratios caused by differences in the physical properties of side chains along the backbone but on the spatial distances between the charged site holding the electron and the backbone amide units. The predictions of this model are tested using ECD and ETD data from derived from experiments carried out using simultaneous infrared photo-activation of the parent ions. Such activated-ion (AI) experiments are thought to disrupt much of the parent ion's secondary structure, which we believe allows us to make more reliable estimates of distances between the charged sites and the various amino acids’ amide groups. The abundance patterns predicted based upon the framework described herein are found to be reasonably consistent with the experimental data. However, the data also provide evidence that internal solvation of the peptide's charged sites remains intact even under AI conditions, and that some of these solvated-ion structures (those involving a charged Lys or N-terminal amine) contribute incrementally to the abundances of fragment ions arising from cleaving nearby NCα bonds. As a result, we conclude that ECD and ETD fragment ion abundances are determined by a combination of factors: (i) internal solvation of charged sites, (ii) spatial distributions or Rydberg orbitals charge densities within several residues of charged sites, and (iii) variations induced by differences in physical properties of side chains. It is primarily the first two of these three that the present paper addresses.