This dissertation presents efforts to expand the role of mass spectrometry (MS) in structural biology. Determination of quaternary structure of a protein complex has been hindered by limited fragmentation from collision-induced dissociation (CID). As an alternative, surface-induced dissociation (SID) was implemented for a quadrupole - time-of-flight instrument in the Wysocki laboratory. This research tested the hypothesis that SID should produce fragmentation reflective of subunit organization. Furthermore, ion mobility (IM) was used to prove the direct relationship between precursor conformation and observed dissociation patterns, and the relationship between activation and product ion conformation. The structure and dynamics of a dimeric small heat shock protein (sHSP) with no solved structure was investigated. The importance of N- and C-terminal domains for dimerization was determined, and the dimers were shown to exchange subunits. From exchange kinetics it is proposed that subunit exchange is unrelated to heat shock activity. SID was used to elucidate the subunit architecture of heterogeneous protein assemblies, including one previously solved protein structure and two formerly uncharacterized proteins. The heterohexamer toyocamycin nitrile hydratase dissociated into trimers, revealing the hexamer to be a dimer of trimers. The bacterial ribonuclease toxin:antitoxin tetramer was shown to have an antitoxin dimer at its core, with flanking individual toxin subunits. The examples presented here are the first clear proof that SID results can clearly indicate the substructure of a protein assembly.IM was used to study the conformation of precursor and product ions. A greater understanding of the relationship between precursor conformation and observed dissociation patterns was developed. Different charge states of a dodecameric sHSP were found to have significantly different conformations, which were directly reflected in SID spectra. IM comparison of CID and SID product ions showed that the same charge state of a product ion from either method has the same CCS. This suggests the product ion conformation is dependent upon ion charge state, and independent of activation method and collision energy. The cause and effect relationship between precursor conformation and MS/MS patterns, and activation and product ion conformation were clearly illustrated. Together, this body of research expands the role of MS for structural biology.

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