Ionic detergents:

• Contain a head group that is either positively charged (cationic) or negatively charged (anionic)
• Have a harsher effect than nonionic detergents because of their ability to bind to protein molecules, altering the protein’s structure and charge 
• Are highly denaturing
• Preferred for use in processes such as gel electrophoresis that require the protein structure to be modified and the cellular structures disrupted 

Nonionic detergents:

• Contain an uncharged head group
• Are less harsh as compared to ionic detergents because of their limited ability to bind to protein molecules and break protein-protein interactions
• Are non-denaturing.
• Are well suited for breaking lipid-lipid and lipid-protein interactions but not suited for breaking protein-protein interactions
• Preferred for use in processes that require the protein structure to be kept intact.