At the Large Hadron Collider (LHC), protons are collided together at extremely high energies. Protons are composite particles made up of smaller particles called quarks and gluons.
While it is true that the fundamental entities described by quantum field theory are fields, particles such as quarks and gluons are excitations or quanta of these fields. In the case of the proton, it consists of a combination of three quarks—two up quarks and one down quark—held together by the strong force mediated by gluons.
When protons are accelerated to high energies and collided at the LHC, it is the interactions between the constituent quarks and gluons within the protons that are being probed. The collision energy is transferred to the quarks and gluons, and various processes occur, such as the creation of new particles, the fragmentation of quarks and gluons into sprays of particles (jets), and the exploration of the properties of the fundamental forces and particles of the Standard Model of particle physics.
So, while the fundamental description of nature is in terms of quantum fields, the LHC collides protons, which are composite particles composed of quarks and gluons, in order to study the behavior of these particles and the underlying fundamental interactions.