The experiment is called the Large HADRON Collider.
Protons are hadrons with a positive charge. So Protons are used in the experiment.
(The same 27km tunnel used to house the previous experiment, Large Electron and Positron collider. Guess what particles were used?)
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Due to their stability and large mass (relative to electrons), protons are well suited to use in particle colliders such as the Large Hadron Collider at CERN and the Tevatron at Fermilab. Protons also make up a large majority of the cosmic rays which impinge on the Earth's atmosphere. Such high-energy proton collisions are more complicated to study than electron collisions, due to the composite nature of the proton.