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By A. Andreatti, W. Stoll

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Has been used in a variety of ‘top-down’ studies of model proteins [83,86,89–91,113], and in the identification of a priori unknown proteins in complex mixtures using database searches against in silico product ion mass ­spectra predicted from whole proteins [80,81]. 7b). 7a precluded confident interpretation. However, simplification of the product ion spectrum with ion/ion reactions allowed fragment ions to be assigned without charge state ambiguity. ‘Top-down’ protein identification via either CID or ETD followed by the examination of low mass product ions has been demonstrated also on instruments with moderate upper mass-to-charge limits (m/z = 2000–4000 Th) after all the product ions were reduced to largely singly-charged states [92,93,123].

Implementation of ion/ion reactions external to the mass spectrometer separates physically the ionization process and ion/ion reactions from the mass analysis step. Advantages derived from this separation include the simplicity with which such ion/ion reactors can be adapted to any mass spectrometer coupled with ESI, independent optimization of mass analysis, and virtually no limits are imposed by the characteristics of the mass analyzer on the kinds of ions that can be used as reactants. However, reaction conditions can be difficult to define in reactors operating at near atmospheric pressure due to the existence of a complicated reaction environment, where a mixture of ions, solvent vapors, and atmospheric gases are present in the reaction region.

Ciamician’ University of Bologna Bologna, Italy Contributors Luca Raveane CNR-ISTM Corso Stati Uniti 4 Padova, Italy Gavin E. Reid Department of Chemistry, Biochemistry and Molecular Biology Michigan State University East Lansing, Michigan Jean-Marie Schmitter European Institute of Biology and Chemistry University of Bordeaux Pessac, France James H. Scrivens Department of Biological Sciences University of Warwick Coventry, United Kingdom Peter Frøhlich Staanum Department of Physics and Astronomy University of Aarhus Aarhus, Denmark John A.

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