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Protonation is the addition of a proton (H+). Conversely, deprotonation is the removal of a proton (H+). Protonation occurs for bases, while deprotonation occurs for acids. The percent protonated is the amount of base that gets a H+ in the process of the reaction. If it's strong, the percent will be assumed to be 100% while if it's weak it will be much lower. You can calculate this by dividing the concentration of the conjugate acid by the initial concentration of the base.