Proto Shopkeepers are a failed, distorted clone of the Original Man. The successful clone of the Proto Shopkeeper is known simply as the Shopkeeper. They are found in large quantities in The Mothership.
Proto Shopkeepers are produced from spawners in The Mothership, among the occasional actual Shopkeeper. They come out of the spawner stumbling around normally, but when damaged, will fall to the floor and start flailing about, akin to a fish out of water. When enough time is elapsed while the Proto Shopkeeper is like this, their head will enlarge and they will explode violently.
Proto Shopkeepers are failed clones of the Original Man, who is believed to be the massive shopkeeper at the top of The Mothership. As the clones of the Original Man are of varying degrees of success, these Proto Shopkeepers are the clones who did not come out properly like standard Shopkeepers do.