Two ways to do this:
1. add "shotDamage" instance variable to your shot sprite. When shot is created, set shotDamage to some number (how much damage it should deal).
When shot hits an enemy, subtract shotDamage from enemy's health.
2. When shot hits the enemy, compare shot's animation name and/or animation frame and decide how much damage it will deal.
Something like this:
Shot On collision with Enemy
...Shot animation "BigBullet" is playing -> Enemy subtract 100 from health
...Shot animation "SmallBullet" is playing -> Enemy subtract 20 from health