The model shows electrons and positively charged particles (not specifically protons).
Thomson Plum: Cathode Ray Experiment
Gas discharge tubes were used, rays emitted from the tube. Thomson placed positive and negative plates next to the tubes. They rays were attracted to the positive plate and repelled from the negative plate.
Ernest Rutherford: Gold Foil Experiment
Alpha particles were shot at a gold foil. Some of the alpha particles ripped straight through the gold foil like Rutherford predicted. Most of the alpha particle bounced off the gold foil. Rutherford was astonished.
Positively charged particles are being shot through the gold atom. Some of them got reflected.
Ernest Rutherford: Around 1911 - Gold Foil Experiment