Mass spectrometry (MS) is emerging as an important tool for studying protein and protein complexes. When applying this tool, it is important to understand and investigate whether some of the intramolecular and intermolecular interactions of proteins in solution and are maintained in the gas phase. To investigate if some of these interactions are maintained in the gas phase, we develop and use a method in which the electron-transfer dissociation (ETD) spectra of native proteins are compared with spectra from ETD followed by low amplitude collisional induced dissociation (CID). From these experiments, we find that some intramolecular interactions from solution are maintained in the gas phase for ubiquitin and beta-2-microglobulin (β2m). However, using these approaches, cytochrome c’s structure in the gas phase appears to be quite different than its structure in solution. We also investigated if ETD spectra of intact protein complexes reflect contact site information in these complexes