There is a long history about what makes up matter starting with Democritus in Ancient Greece and continuing through modern times. A critical experiment that spurred many future experiments was Rutherford's discovery of the nucleus in 1911. This experiment used a simple collision between Helium nuclei and gold foil and demonstrated the existence of the nucleus.

Thomson's “Plum Pudding” Model of the Nuclues

Prior to this experiment, the leading theory of what made up atoms is credited to J.J. Thomson. Previous experiments discovered the existence and some of the properties of the electron, but we unable to resolve details of the atom itself. Thomson suggested that matter was like a plum pudding where the negative electron “raisins” were suspended in a pudding-like positively charged, low density “pudding”.

Ernst Rutherford hypothesized that if he could send charged particles into some form of matter that the small deflections due to the interactions with the negatively charged electrons would confirm his atomic theory. That is, Rutherford and his team went out to validate the model of atoms that were informed by their (and others') previous experiments and the leading models of the day.

Rutherford and his team were aided in their work by the recent discovery by