Humans discover particles occurring in natural processes. To identify definite, discrete units such as atoms and molecules it takes experiments that integrate into material events that are happening naturally. As with the radioactivity of Becquerel so with the discovery of the electron by J.J.Thompson in 1887 – what we find occurring makes most sense as an interacting particle of matter. How all this comes together in Rutherford’s gold foil experiment of 1911 as an atomic nucleus is inferred from how alpha particles scatter.
What something is made of is all the essential realities that come together as that object. The universe functions very differently from human actions as deep, continuous, energies that come together through quanta to make matter, mass, elementary particles and atomic nuclei. Different energies come together as the various specific elementary particles interacting. So that it is possible to comprehend all the different elementary particles as functions of the energies that come together to make them.
Super Kamiokande detection of neutrino through Cherenkov Radiation