Infrared spectroscopy of fragments of protonated peptides: direct evidence for macrocyclic structures of b5 ions.

b ions are of fundamental importance in peptide sequencing using tandem mass spectrometry. These ions have generally been assumed to exist as protonated oxazolone derivatives. Recent work indicates that medium-sized b ions can rearrange by head-to-tail cyclization of the oxazolone structures generating macrocyclic protonated peptides as intermediates. Here, we show using infrared spectroscopy and density functional theory calculations that the b(5) ion of protonated G(5)R exists in the mass spectrometer as an amide oxygen protonated cyclic peptide rather than fleetingly as a transient intermediate. This assignment is supported by our DFT calculations which show this macrocyclic isomer to be energetically preferred over the open oxazolone form despite the entropic constraints the cyclic form introduces.