What Abdallah has said is absolutely right.

A standard example is the binding energy calculation of He4. It is made out of two protons and two neutrons. Masses are measured in atomic mass units where carbon is a reference point. One u is mass of carbon atom/12.

Mass of two protons is 2x1.00728=2.01456 u.

Mass of two neutrons is 2 x 1.00866=2.01732 u.

Mass of two electrons= 2 x 0.000549 = 0.001098 u.

total mass is 4.032978 u.

mass of the alpha particle is, 4.00153 u, that is the difference is 0.031448 u. Therefore the binding energy of alpha particle is 0.031448 x 931.5=29.29 MeV (approx). If you do not like to include masses of the electrons then the defect is 0.03035 u. This corresponds to a binding energy of 28.27 MeV (approx).

In order to let Einstein's E=mc² being right (and this is the sole reason), one invented that a neutrino is formed by the decay of a neutron into a proton and an electron (beta-decay). Indeed, a neutron is heavier than the sum proton + electron, and taking into account the equivalent mass of the binding energy, something doesn't fit.

However, no experiment involving decaying neutrons into protons and electrons (beta) prove this.

The Cowan–Reines neutrino experiment supposing to "prove" this was a farce, because, it made a circular reasoning without any physical proof of the generation of antineutrinos that would result in the production of neutrons and positrons, out of protons and antineutrinos.

More neutrino's were hypothesized, only because of the discrepancies with the masses of the constituants in reactions. Quantum mechanics became a cook book.

This is an example of a biased way of practicing science, especially in physics. Hence, your question still remains open.

Binding energy is well established from early years of atomic research. The mechanism by which it operates can be as complicated as you like in terms of quarks and gluons. A little simpler is the source of the binding energy. It is the strong nuclear force that only acts at short range.

The question arises about how a short range force can alter a long range property like mass, and so perfectly that atomic mass, inertial mass, and gravitational mass are all altered by exactly the same amount. The answer seems to be that the strong force operates on the stress energy of space to decrease it locally, and the altered curvature propagates to far distance. It is just another way of saying the missing mass has been converted into binding energy, and the associated fields spread out into space. 

There are even more questions behind the initial question which are not clearly answered and might be related in the long term.

1) Take simple case of Hydrogen atom, why there is no "radiative collapse" of the electron who normally should crash towards nucleus so who gives additional energy for the electron to orbit stable

2) From electrical charge, the electron and proton have the same except opposite polarity but what is the impact or root cause that proton's mass is much higher that electron's mass