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Fragmentation efficiencies of various ‘activated-ion’ electron capture dissociation (AI-ECD) methods are compared for a model system of bovine ubiquitin 7+ cations. In AI-ECD studies, sufficient internal energy was given to protein cations prior to ECD application using IR laser radiation, collisions, blackbody radiation, or in-beam collisions, in turn. The added energy was utilized in increasing the population of the precursor ions with less intra-molecular noncovalent bonds or enhancing thermal fluctuations of the protein cations. Removal of noncovalent bonds resulted in extended structures, which are ECD friendly. Under their best conditions, a variety of activation methods showed a similar effectiveness in ECD fragmentation. In terms of the number of fragmented inter-residue bonds, IR laser/blackbody infrared radiation and ‘in-beam’ activation were almost equally efficient with ~70% sequence coverage, while collisions were less productive. In particular, ‘in-beam’ activation showed an excellent effectiveness in characterizing a pre-fractionated single kind of protein species. However, its inherent procedure did not allow for isolation of the protein cations of interest.

A Variety of Activation Methods Employed in “Activated-Ion” Electron Capture Dissociation Mass Spectrometry: A Test against Bovine Ubiquitin 7+ Ions