QFT seems very well suited to handle scattering amplitudes between particles represented by the fields in the Lagrangian. But what if you want to know something about a bound state without including it as an extra field? For example, suppose we have electron+proton QED (ignoring the proton's structure):
$$\mathcal{L} = -\frac14 (F_{\mu\nu})^2 + \bar{\psi_e} (i\not \partial -m_e)\psi_e + \bar{\psi_p} (i\not \partial -m_p)\psi_p - e \bar{\psi_e} \not A \psi_e + e \bar{\psi_p}\not A \psi_p$$
I can use this with no problem to calculate Rutherford scattering or similar processes. But this Lagrangian should also have the hydrogen atom hidden in it somewhere. For example, I may want to use QFT to calculate the binding energy of hydrogen. Or I might want to calculate the probability of firing an electron at a proton and getting hydrogen plus photons as a result. How can this be done? Obviously this is a broad subject, so I'm just looking for an outline of how it goes.