Infrared multiple photon dissociation (IRMPD) spectroscopy was used to study formation of b 2 ϩ from nicotinyl-glycine-glycine-methyl ester (NicGGOMe). IRMPD shows that NicGGOMe is protonated at the pyridine ring of the nicotinyl group, and more importantly, that b 2 ϩ from NicGGOMe is not protonated at the oxazolone ring, as would be expected if the species were generated on the conventional b n ϩ /y n ϩ oxazolone pathway, but at the pyridine ring instead. IRMPD data support a hypothesis that formation of b 2 ϩ from NicGGOMe involves mobilization and transfer of an amide position proton during the fragmentation reaction. E ffective application of tandem mass spectrometry, collision induced dissociation (CID), and bioinformatics for protein identification requires a clear understanding of peptide ion fragmentation mechanisms. Low-energy CID of protonated peptides promotes rearrangement reactions in which the added proton presumably migrates to the amide bond that is ultimately cleaved [1][2][3][4][5][6][7][8][9][10][11][12], as treated in the "mobileproton" (MP) [13][14][15][16][17][18][19][20][21][22][23][24][25], and "pathways in competition" (PIC) models of peptide dissociation [26]. Experimental studies have established that the C-terminus-containing y n ϩ fragments are truncated peptides [6,27,28], while the N-terminus-containing b n ϩ and a n ϩ species have substituted oxazolone ring and imine structures, respectively [4,5,11,12,29,30].Wavelength-selective infrared multiple photon dissociation (IRMPD) spectroscopy has recently been used to probe and confirm proposed structures of peptides and peptide dissociation products, with studies of the latter focusing primarily on b n ϩ and a n ϩ ions [11,12,29,30]. Our group has designed model peptides and approaches to probe intramolecular migration of protons during peptide dissociation reactions [31,32]. Versions of these model peptides are the subject of the present study, in which IRMPD was used to determine the structure of protonated nicotinic acid-glycine-glycinemethyl ester (NicGGOMe), and the b 2 ϩ fragment ions from NicGGOMe and benzoic acid-glycine-glycinemethyl ester (BzGGOMe). The pyridine ring of the nicotinic acid residue is used to sequester the "mobile" proton added to the peptide to produce (M ϩ H) ϩ , and inhibit migration to the site of intramolecular nucleophilic attack during fragmentation reactions. IRMPD spectroscopy provides strong evidence for the mobilization and migration of amide-position protons during dissociation reactions of model peptides.
Experimental
Mass Spectrometry and IRMPD SpectroscopyCID experiments were performed using a ThermoFinnigan (San Jose, CA, USA) LCQ-Deca quadrupole ion trap (QIT) mass spectrometer. IRMPD spectra were collected using the FT-ICR mass spectrometer coupled to the beamline of the free electron-laser user facility (FELIX) infrared free electron laser [33][34][35]. Ions produced by electrospray ionization (ESI) were accumulated in a hexapole ion trap, and isolated and irradiated with FELIX for 2 s at a...