1 Anion Dependence in the Partitioning between Proton and Electron Transfer in Ion/Ion Reactions Joshua J. Coon,* 1,5 John E. P. Syka,* 2,3 Jae C. Schwartz, 3 Jeffrey Shabanowitz, 1 Donald F. Hunt, 1,4 Departments of Chemistry 1 and Pathology 4 , University of Virginia, Charlottesville, VA Engineering Physics Program, 2 University of Virginia, Charlottesville, VA Thermo Electron Corporation, 3 San Jose, CA * J.J.C. and J.E.P.S. contributed equally to this work. 5 To whom correspondence should be addressed. Email: jcoon@virginia.edu . Phone: (434) 924-7994. Fax: (434) 982-2781. Dept. of Chemistry, Univ. of Virginia, McCormick Rd., Charlottesville, VA 22901 Keywords: electron transfer dissociation, electron capture dissociation, fragmentation, ion/ion reactions, charge transfer, ion trap Abstract Gas-phase reactions of singly-charged anions with multiply-protonated peptides, in a RF quadrupole linear ion trap, leads to either peptide deprotonation (proton transfer) or electron deposition (electron transfer). The former process induces peptide backbone cleavage through a reaction scheme analogous to electron capture dissociation (ECD). Here we characterize the preferred reaction pathways of several anions with multiply-protonated peptides. These anions include sulfur dioxide, perfluoro-1,3- dimethyl-cyclohexane, sulfur hexafluoride, anthracene, and 9,10 diphenylanthracene. In our ion/ion apparatus, we find some anions react exclusively via proton transfer, others react by proton and electron transfer, while another behaved predominantly as an electron transfer agent. 1. Introduction Owing to its non-ergodic nature, electron capture dissociation (ECD), introduced by McLafferty and co- workers [1], has been unique among ion fragmentation methods. In ECD near-thermal electrons, contained by the magnetic field of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, are captured by multiply-charged peptide/protein cations. The process induces cleavage of the amide nitrogen-alpha carbon bond to create c/z-type product ions, [2,3] while preserving labile post-translational modifications. [4-11] Unfortunately, simultaneous confinement of electrons and positive ions is not straightforward in other trapping mass analyzers, e.g., quadrupole ion traps; hence, ECD remains restricted to FTICR systems – unavailable to the vast majority of the biological mass spectrometry community. Cations and anions can, however, be contained concurrently in radio frequency (RF) electrostatic trapping fields. By exploitation of this attribute, we recently reported the use of anions as vehicles for electron delivery to multiply-protonated peptides in a RF quadrupole linear (QLT) ion trap mass spectrometer [12]. In ECD, charge neutralization and hydrogen atom release results from the capture of near-thermal electrons by peptide cations (excitation energy ~ 6 eV) [13]. Likewise, the electron transfer reaction deposits sufficient excitation energy, only lowered by the electron affinity (EA) of the radical anion (0.5 – 1.5 eV, depending on the radical anion), for hydrogen atom liberation. [12] In either case, the net effect is production of mobile hydrogen atoms for subsequent recombination, producing c/z-type fragmentation. Over the past decade McLuckey, Stephenson, and co-workers have pioneered ion/ion chemistry using three-dimensional (3D) quadrupole ion traps (QIT) [14-20]. Those experiments employ proton transfer reactions for peptide/protein charge neutralization [21- 26]. This work was the primary, but not exclusive [27,28], basis for the prevailing view that multiply- charged peptides interact with anions exclusively via anion attachment or proton transfer. Our recent report extends ion/ion chemistry to contain a new reaction pathway: electron transfer [12]. Here we characterize the ion/ion chemistry of several anions with multiply- protonated peptides, as observed with our QLT ion/ion apparatus. Some of the anions were used by others (e.g., sulfur dioxide and perfluoro-1,3-dimethyl- cyclohexane); some of the anions were not (e.g., 9,10 diphenyl anthracene). In addition to anion characterization, we briefly comment on the differences between 3D RF quadrupole ion traps (QIT) and RF quadrupole linear ion traps (QLT) for ion/ion reactions.