it was found that the mass of electrons, which had recently been discovered, was very much less than the mass of atoms so they must be sub-atomic particles, then an experiment showed that most of the alpha particles directed at thin gold foil passed through but a few bounced back, suggesting the positive charge was concentrated at the center of each gold atom. and finally discovery of neutrons in the nucleus which explained why the mass of atoms was greater than could be accounted for by the mass of the protons.