| Tandem mass spectrometry (MS/MS) has become an important analytical tool in the elucidation of biological polymers. Recently, there has been a considerable effort to extend MS/MS to the investigation of biological, noncovalent complexes with the hope that tandem mass spectrometers could serve as gas-phase laboratories where large, biological complexes could be isolated, and multiple components of the complex could be consecutively removed to reveal information regarding the structure of the complex.;A series of investigations are made into the feasibility of using MS/MS for the characterization of biological complexes. A 9.4 tesla, narrow-bore Fourier-transform mass spectrometer was constructed for these experiments having ultra-high resolution and the capability of multiple stages of tandem mass spectrometry with a wide range of possible dissociation energies. The investigations were done using simple biological complexes, namely nonspecific protein homodimers and homogeneous clusters of peptides.;Charge partitioning in protein homodimers is shown to be a function of several parameters using protein homodimers as the test complex. These parameters include the gas-phase charge state of the complex, the composition of the electrospray solution from which the complex is formed, and the gas-phase conformational flexibility of the complex with the more flexible monomeric unit removing a majority of the complex charge. Furthermore, it is shown that in some cases, the charge partitioning of a specific charge state of a protein homodimer depends upon whether the charge state is formed directly by electrospray ionization or by gas-phase charge reduction of more highly charged homodimers.;To compare the dissociation processes of noncovalent complexes of different sizes, multiply charged peptide clusters are examined by MS/MS. It is shown that the dissociation of smaller peptides resembles the dissociation of atomic clusters and amino acids while the dissociation processes of larger peptides are largely determined by their conformational flexibility, thus marking the point at which structural properties of individual components in the cluster begin to dominate over bulk properties in determining the cluster dissociation pathways.;An alternative mass spectrometry based method for the elucidation of biological polymers, not requiring potentially disruptive dissociation techniques, is gas-phase H/D exchange. This method is investigated as a technique for studying noncovalent complexes using sodium adducted peptides and peptide dimers. It is shown, that the rate and extent of gas-phase H/D exchange of noncovalent complexes is greatly influenced by the primary structure of the peptides in the complex and the number of adducted metal ions.;The results of these investigations suggest that current MS/MS methods are not well suited to the elucidation of the solution-phase structure of biological complexes. While exceptions exist, MS/MS results of biological complexes should not in general be expected to provide detailed solution-phase structural and energetic information. |
