Most of the mass of matter comes from energy of strong force interactions between quarks. However the quarks still have intrinsic mass. Other particles have no intrinsic mass but still have energy. So according to mass-energy equivalence, these particles should still have effectively mass, to my understanding. If so, how can we label a particle as massless or not if they all have mass due to energy they carry? Doesn't mass of quarks come from energy too?