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The need to push the LHC beyond its limits and increase the deliverable luminosity to the experiments by about one order of magnitude has driven the ongoing injector and HL-LHC upgrades. The higher luminosity requires to increase the beam brightness, which directly translates in the need to adapt the different machine protection systems. Among all the foreseen upgrades, the transfer line collimators (TCDI) and the LHC injection protection systems will be revised. In particular, the guaranteed protection is evaluated in this Ph D work, together with the specification for the minimum shielded aperture in case of injection failures. A detailed model is also developed which insures a more reliable and efficient procedure for the validation of the TCDI setup within the required accuracy. The physics beyond colliders will also be pushed over its current limits in the HL-LHC era. SHiP, a new proposed fixed target experiment served by the SPS is under study. The unprecedented level of requested protons on target per year needs an assessment of the present SPS slow extraction. The main performance limitation of this technique is the activation of the area surrounding the extraction elements due to losses. The possibilities to optimise the present slow extraction as well as new ideas are investigated in order to preserve today's performances while reducing the extraction losses.