In school you learn something along the lines of a proton has a "weight 1 of atomic unit". Well, turns out, if you take the proton parts (quarks and whatnot), the weights just don't add up. That we found out in school because we were nerds already back then.
New measurements go much beyond that. "Dissecting the mass of the proton" is an entertaining read:
Nearly all the mass of known matter is contained within protons and neutrons—the particles that make up the nuclei of atoms. But how do the protons and neutrons acquire their mass? Each of these particles, or “nucleons,” is composed of a dense, frothing mess of other particles: quarks, which have mass, and gluons, which do not. Yet the quark masses only add up to a mere 1% of a proton or neutron’s mass, with the bulk of the proton mass coming purely from the motion and confinement of quarks and gluons.