Let's add "at rest" to the end of your question: "I suppose each proton/neutron is unique in terms of its mass/energy content" Oh boy, so there's a can of wor

Let's add "at rest" to the end of your question: "I suppose each proton/neutron is unique in terms of its mass/energy content" Oh boy, so there's a can of worms. "Unique" would need to be nailed down to test that statement, and runs into some observational problems in that atoms exist and can be found in things like monatomic gasses in enormous enough quantities that you can wash out any contributions from other matter. These gas clouds can be measured and manipulated, and have been. The results limit the variation from proton to proton (and climbing the periodic table of elements, from nucleus to nucleus) to be entirely negligible. Theory depends on where you look. Protons are usually taken to be indistinguishable particles (each proton obeys the same particle statistics at low energy). Additionally, there are good reasons to believe that any distinguishability -- however small -- leads to observables (an example is elucidated and generalized in the "Bosonic Birthday Paradox" http://arxiv.org/abs/1106.0849 http://arxiv.org/abs/1106.0849 ). Those observables are not seen. Proton distinguishability also goes to the question of the mechanisms by which the Pauli Exclusion Principle manifests. It does manifest among protons in atomic nuclei, which is important. Retaining that and introducing actual distinguishability at small scales is a challenge. If protons are (barely) distinguishable to us in experiments, they'll be (barely) distinguishable in decays and in electron interactions too. But if you think of a proton as "a mess"[1] and look at it at, say, the QCD scale, your question might be better put as,"how do confinement (and asymptotic freedom) and colour exchange work?". Peering into the structure of a proton at that scale is certainly interesting, but any information in there can only escape in ways permitted by confinement. [1] http://profmattstrassler.com/articles-and-posts/particle-physics-basics/the-structure-of-matter/protons-and-neutrons/ http://profmattstrassler.com/articles-and-posts/particle-phy...