Specialist Physics Seminar Tuesday 27 May 2003 at 11.30

Electron capture dissociation reveals secondary structure of polypeptides

Nick Polfer

School of Chemistry, Edinburgh, United Kingdom


Fragmentation techniques in mass spectrometry are widely used to establish sequence infomation of polypeptides and hence identify proteins. Electron capture dissociation (ECD) is a novel fragmentation technique which is believed to work on a non-ergodic process (i.e. fragmentation before randomisation of energy). The 'hot hydrogen mechanism' proposed by McLafferty postulates electron capture at the hydrogen of the protonated site followed by H atom transfer to a high affinity site (e.g. backbone carbonyl), where backbone cleavage occurs.

This work aims to show that the relative transfer efficiency (and therefore cleavage efficiency) is related to the gas-phase basicity of the protonated site (inversely) and the secondary structure of the peptide. Modelling of the gas-phase structures using the AMBER force field model indicates that hydrogen bonding of the protonated site to particular backbone carbonyls enhances H atom transfer. Hence ECD is not limited to primary structure information of the peptide (i.e. amino acid sequence), but also yields higher structure information of the peptides.