How are the protons for collisions in the LHC made? I heard that the LHC smashes two protons together to research the universe.
But how does it create the protons for collision? If we strip off the electrons won't there be neutrons along with protons?
A "Duoplasmatron source" is used by the LHC, it ionises atoms into negative or positive ions but how is the proton separated from that?
 A: See this article on the LHC proton source.
Hydrogen gas is ionised using a strong electric field, and the resulting protons are accelerated and focused then injected into a linear accelerator.
A: From the horse's mouth:

The proton source is a simple bottle of hydrogen gas. An electric field is used to strip hydrogen atoms of their electrons to yield protons. Linac 2, the first accelerator in the chain, accelerates the protons to the energy of 50 MeV. The beam is then injected into the Proton Synchrotron Booster (PSB), which accelerates the protons to 1.4 GeV, followed by the Proton Synchrotron (PS), which pushes the beam to 25 GeV. Protons are then sent to the Super Proton Synchrotron (SPS) where they are accelerated to 450 GeV.
The protons are finally transferred to the two beam pipes of the LHC. The beam in one pipe circulates clockwise while the beam in the other pipe circulates anticlockwise. It takes 4 minutes and 20 seconds to fill each LHC ring, and 20 minutes for the protons to reach their maximum energy of 4 TeV. Beams circulate for many hours inside the LHC beam pipes under normal operating conditions. The two beams are brought into collision inside four detectors – ALICE, ATLAS, CMS and LHCb – where the total energy at the collision point is equal to 8 TeV.

