Non-covalent protein complexes: Non-covalent interactions between the molecules are usually disrupted during ionization. ESI, however, has proved to be sufficiently soft for allowing detection of the protein complexes. It is, however, important to note that the complexes of biomolecules detected in gas phase may not represent the true solution complexes. The structures of the molecules in solution and the interactions they are involved in are determined by the complex interplay of hydrogen bonding, hydrophobic interactions, van der Waals forces, and electrostatic interactions. In gas phase under high vacuum , the electrostatic interactions are usually the most predominant ones. One therefore has to be careful while analyzing the data for the non-covalent complexes.

Three dimensional structures of proteins and peptides: Mass spectrometry can provide information about the three dimensional structure of a protein. Consider a protein that is being analyzed using ESI-MS. An unfolded protein usually shows a broader charge distribution with higher amount of charge due to larger solvent-accessible area and the exposed ionization sites. Another approach includes structural analysis of the proteins after subjecting them to the conformation sensitive reactions. Hydrogen-deuterium exchange (H/D exchange) is the most widely used such reaction. The exposed regions on a protein will readily exchange their amide hydrogens with deuterium. The amides that are involved in backbone H-bonding ( i.e. those involved in secondary structures) exchange their hydrogens very slowly. The folded regions in the protein can then be identified by analyzing the peptide fragments using tandem mass spectrometry. These approaches also allow study of the folding processes of proteins.