Short, hopefully clear answer: They found that the proton was composed of smaller constituents (quarks) which carried, on average, one-third of the proton's mass each, suggesting 3 quarks in the proton or neutron. The early experiments gave information coming from all 3 quarks together, and were not able to tell if they were identical or different, or if they were different for the proton and neutron.

Once you have a model of protons and neutrons as being composed of three quarks, then there have to be differences since the proton and neutron are different (i.e. different charge), and it's natural to have the idea of two different kinds of quarks, up with charge +2/3, and down with charge -1/3. 

That leaves out a lot of details, and refers to early measurements in general, rather than a specific set of measurements. The evolution of our understanding isn't limited to just these measurements, and I'm not trying to portray a historically accurate picture of how our picture evolved. Some technical details are incorrect but should give, I hope, the correct idea without getting into details.

@john

Thanks for the answer. The crucial part I was looking for was on "average one third of the mass of the proton each" that does not exclude same particle masses and so is consistent with 3 anti down quarks ( of diffrering colour).

As far a s the neutron is concerned there do not have to be differences becuase the neutron is just a proton with an orbiting electron. NB. Neutron decay

https://www.researchgate.net/publication/253298817_Harmonic_quintessence_and_the_derivation_of_the_charge_and_mass_of_the_electron_and_the_proton_and_quark_masses

Article Harmonic quintessence and the derivation of the charge and m...

Well, as I'm sure you know, the idea of the neutron as a proton orbiting and electron is not consistent with our conventional understanding of physics.  Also, one of the simplifications in my answer is saying that we see three constituents, each with an average of 1/3 of the proton's mass. First, we do not see constituents of fixed mass, so saying the proton is simply 3 massive (m~300 MeV/c) quarks has problems. In addition, when probing the proton at higher energies, where there is more sensitivity to the basic constituents, we do not see massive constituents, we see nearly massless constituents.

Current and Constituent masses:-

In high energy experiments probing the structure of proton or neutron via deep inelastic scattering, the smaller masses which match experiments  are called "current quark masses" which are  only about  few MeV for up quarks and few-10 MeV for down quarks. You may refer to any PDG data table for reference. 

That each of the quarks in the 'uud' combination of proton  or 'udd' combination of neutron has an average mass  m_u \sim m_d \sim  300 MeV is derived from the 'static' quark model of hadrons due to Gell-Mann and Zweig that also predicts 'baryon octet' , 'baryon decuplet', 'meson octet' etc. based upon SU(3) global isospin flavour symmetry e.g.

3-barX3=1+8,   3X3X3=10+8+8+1 etc. Fitting the known hadron masses

through the corresponding mass formulas of quark model gives these masses of quarks which are knon as "Constituent Mass".

@John

Thanks for that 

But it is the electron that orbits the proton in the neutron. And in what way is that not consistent exactly, with conventional thinking.

First, the hydrogen atom gives the size scale for the binding of an electron and a proton, and there's no conventional way to have the electron bound so tightly that the radius goes from ~10,000 fm to ~1 fm.  On a more basic level, if the neutron were a bound system of a proton and an electron, it's mass should be lower than the sum of the proton and neutron masses, but it is higher.

Dear DR. Worley

I have followed the standard path being followed in particle physics which has been universally accepted. The model for neutron with a proton core and a circulating orbittal electron is not universally followed. If you have such a model it has to be examined in detail and its consequences has to be worked out. I had a cursory look at your paper but at present I have no time to follow it.

Best Wishes for Your new model,

@John,

The classical radius of the electron is about 1fm- no problem there.

We are using a relativistic additive model for mass - exact answers for the mass of the neutron result are obtained.

The classical radius of the electron is not relevant to the size of a bound proton-electron system.

If the neutron were simply an electron orbiting a proton, then the neutron mass would be lower than the proton+electron mass. If you model gives a lighter neutron mass, then it could be that this bound state exists within your model. But using the true masses, this is not the case.

@ John

I am getting fixed ideas not explanations.

The classical radius of the electron is about 1fm- no problem there- very relevant similar radii to the radius of the neutron

We are using a relativistic additive model for mass - exact answers for the mass of the neutron result are obtained.

There is no reason to subtract the mass of the electron from the mass of the total system- totally illogical.

The classical radius of the electron has no physical significance that I am aware of, and in any case has nothing to do with the size of a proton+electron bound state. You can't conclude that n = p + e simply from knowing the masses and, as I'll explain, the masses show that this is not true.  In any case, you need a mechanism for binding. If that's electromagnetic interactions, then we can calculate the relevant size for the electron orbit, or we can simply look at a hydrogen atom. To have a bound state that's 1,000,000,000,000,000 more compact, as you suggest, would require a new force which is outside any current conventional understanding of physics.

As for the masses, typical bound states (molecule,atom, nucleus) involve massive constituents held together by some force.  The binding of the particles 'removes' energy from the system (converts some of the mass into potential energy), and so one has to put extra energy into the system to overcome that binding energy and break it apart. So the mass of the bound system (nucleus, atom, etc...) is slightly less than the sum of the constituents (protons and neutron for nuclei, nucleus+electrons for atom).  So the natural upper limit for a proton+electron bound state is the sum of the proton and electron masses.  If it's above that, which it is, then saying that the neutron is a bound state of a proton and neutron requires a completely new understanding of what it means to be bound.

I hope that this is sufficient explanation. RG comments is not suitable for a full physics course, so it may not be feasible to give what you consider a sufficiently detailed explanation. I also can't point out specific differences between your model and conventional physics because you haven't provided any explanations, only unsupported assertions that the proton is 3 identical quarks, the neutron is a proton+electron bound state, etc... The fact that you can calculate masses within some model of quark structure of hadrons doesn't mean that that model is correct, especially given that the underlying assumption has no physical explanation and contradicts many observations.

@ John

It is not that i have not studied conventional physics, I have in depth- its just that we should be allowed to question.

We do not know that the classical radius has no significance. in fact if you look at the maths it has plenty, it relates the Bohr radius to alpha, the charge to the mass etc. etc.

On size you repeat yourself as if that is an explanation, 1fm  is nevertheless very close to the neutron radius - that is no coincidence.

There is no new force required, electromagnetic forces are enough -that's why the electroweak marries so well.

You need no new physics to explain the mass, just relativity, the mass of the electron rises considerably with its speed. That accounts for the increase in mass and binding energy.

Interestingly the unsupported evidence comes form yourself "

"They found that the proton was composed of smaller constituents (quarks) which carried, on average, one-third of the proton's mass each, suggesting 3 quarks in the proton or neutron".

You would have supposed by now they would have found different masses - but not so.

A proton with an orbiting electron has a baryon number and a non-zero lepton number. That's not consistent with the conservation of these quantum number, as observed in many processes. A neutron decays into a proton, an electron, and also an anti-neutrino. There is no way to have a dynamical model of the neutron including an anti-neutrino, since it is sensitive to the weak force only.

@Andrew.  You're also ignoring the fact that I said that initial measurements suggested 3 massive constituents, but later measurements using higher energy scattering to probe more deeply found constituents with much smaller masses. Because they are tightly bound and very energetic constituents, it isn't possible to directly measure a mass, but the data basically rule out the idea of ~300 MeV quarks as the fundamental constituents.

@ John,

Well that's  not at all surprising, when you start to deconstruct the quarks.

The principal question remains was there any mass difference between these deconstructed elements?