Rutherford's experiment was the gold foil experiment.
The gold foil experiment was him shooting alpha particles (you could think of this as a Helium atom without its electrons) into a gold foil. The whole experiment was surrounded with something called Zinc Sulfide which sparked when the alpha particles hit it.
Most of the alpha particles went through, approximately 1 in 8000 alpha particles deflected at a large angle (almost right back to where it was shot).
This constant ratio caused him to conclude that:-the atom was mostly empty space (since most alpha particles went through)-there was something very positive in the atom (the proton)-the proton was very dense (since it made something going light speed deflect back at a large angle)-The proton was also very small (since only 1 in 8000 hit it)
Prior to the discovery of the proton, John Dalton's periodic table was used. Having "elements" such as soda and potash. Now that we have discovered the proton and found out that each atom's number of protons is unique, we used that to classify each element's identity.