Mass and energy

I may have said that the Universe was made of energy - but actually the Universe is made up of two things : particles and energy.

Let's first delve into particles.

There are two types of particles, fermions and bosons.  

Fermions are what we call matter. They have all the properties we normally associate with matter, like having mass and taking up space. Two fermions cannot be in the same place at the same time. Scientifically, a fermion is any particle that has half integer spin.

Bosons are also particles, and they have whole integer spin. Bosons are particles, but don't behave like matter at all. A whole bunch of them can be in the same place at the same time. For instance, the most "famous" boson is the photon, the light particle. As a rule, bosons are the "mediator" particles: photons are responsible for electromagnetic force, gravitons for gravity, etc.

Both fermions and bosons are particles, only fermions are matter. It turns out, a property of particles is that most particles have mass (except for the photon, the only massless particle).

Thus all the fermions have mass, this is one of their properties.
Making up the other half of the universe (well, in fact a lot more than half. There is a lot more energy than matter out there, but I regress) is energy.

Now Energy

Energy is a lot harder to pin down, but one of the properties of energy is that it too, has mass.
This is where the "mass deficit" in nuclear reactions comes from. Atoms are bound together with binding energy, when that energy is released it "carries away" its associated mass.
This is a small amount of the mass in an atom. However, if you look at a proton, this mass becomes apparent. A proton has a mass of 938 MeV/c² (normally physicists drop the c² part, but I'll leave it in for now). However, a proton is made up of two up quarks and 1 down quark. The mass of these quarks only add up to ~9 MeV/c^2. That means that about 99% of the mass of a proton actually comes from mass of the energy binding the proton together.

E = mc²

So, to summarize, there are particles and energy. Most particles have mass. E = mc² isn't a statement that "mass can be converted into energy" it is a relation to how much mass energy has.
So matter and mass are not the same thing, it just so happens that matter has mass.

source : How is energy converted into matter? : askscience