It was proven in Prout's hypothesis
William Prout proposed a a hypothesis (called Prout's hypothesis ) which propose that the fundamental positive particle is a charged version of hydrogen. which he called protyle (later called proton. )
He derived this hypothesis through his analysis on experiments using anode tube (or positive ray tube).
Unlike cathode ray tube (in which the ray/beam is made up of electrons) , producing rays/beams using 'positive ray tube' makes it difficult to analyze the fundamental positive particle. This is because there is a variety of particles (depending on what gas sample you ionize) with charge-to-mass ratio that is produced using 'positive ray tube'. (Cathode ray tube, on the other hand, only produce a single charge-to-mass ratio.. indicating it is a single particle.. i.e. electrons).
But what William Prout discovered was that each positively charged particles have charge-to-mass ratio that is multiples of the charged particles produced from hydrogen.
So if "protyles" are the fundamental positively-charged particle, then this should mean that you can synthesize bigger element (higher elements) by combining this "protyles" and neutrons (which was found later). Or alternativelty, you can break nucleus of bigger elements and produce particles made up of "protyles" and neutrons.
I'm not going into quarks, but I;m pretty sure protons have same quark make up.