Pepper was a food seasoning.

Vespiforms were allergic to the active ingredient in pepper, piperine. The Tenth Doctor laced the soup at Eddison Manor with pepper in order to catch a Vespiform. (TV: The Unicorn and the Wasp)

On the Sea Eagle, the Sixth Doctor tried to hide in an empty barrel, except that it was actually full of pepper and it made him sneeze, alerting pirates to his presence. (AUDIO: Doctor Who and the Pirates)