| Mass spectrometry is an analytical tool that can be used to study intact proteins. Although intact proteins may be kilodaltons or more in mass, ionization methods such as electrospray ionization make it possible to introduce these large compounds to the mass spectrometer. Analysis of intact proteins, known as top down proteomics, has the ability to provide the protein mass, partial sequence and identification of post-translational modifications. Each of these can be used to assist in protein identification and characterization.; Tandem mass spectrometry of proteins and peptides has been most commonly carried out using collision induced dissociation (CID). However, in this work, other methods of dissociation are explored. Infrared multiphoton photodissociation (IRMPD) in a quadrupole ion trap offers advantages over CID. CID necessitates tuning specific trapping and excitation voltages to dissociate one mass-to-charge ion, and results in the loss of product ions less than one-third of the mass-to-charge ratio of the parent ion. IRMPD does not have this limitation. No trapping or excitation voltages must be tuned, and a wider mass-to-charge range of product ions is trapped after dissociation. As a result, more structural information about a parent ion can be obtained. Multipole storage assisted dissociation in a quadrupole - Penning trap - linear ion trap - time-of-flight mass spectrometer is also used to dissociate peptides/proteins in a linear ion trap. Like IRMPD, it does not require tuning to dissociate ions and can provide primary structural information.; Dissociation of highly charged protein parent ions can produce highly charged product ions. To identify these product ions, their charge state must be known. Due to limited resolution of the instruments used for these studies, and the large number of product ions formed from dissociation of intact proteins, a new strategy for product ion charge state determination was developed. Simultaneous reactions between all product ions formed from the dissociation of an intact protein and pulsed dimethylamine are used to determine product ion charge state. The product ions undergo proton transfer with the dimethylamine, and the shift in product ion mass-to-charge ratio is used to determine the product ion charge state. |
