There are a few different types of Pro Tools system, the main differences are outlined below:
Pro Tools (non-HD) with Red 4Pre (Thunderbolt mode)
Only the first 32 inputs/outputs on the Red 4Pre will be available when it's connected to this type of system. This is a limitation of non-HD versions of Pro Tools.
Pro Tools HD Native (Pro Tools mode)
Pro Tools HD Native systems include a Thunderbolt interface/PCIe card with DigiLink connectors. With the Red 4Pre in Pro Tools mode and connected to this type of system 32 inputs/outputs will be available per Mini DigiLink connector used, for a total of 64 I/O.*
Pro Tools HD/HDX (Pro Tools mode)
The Red 4Pre will connect to this sort of system in the same way as with an HD Native system, using the Mini DigiLink connectors. Please note that if you're connecting to a legacy piece of hardware that has full size 'DigiLink' connectors rather than 'Mini DigiLink' connectors that you'll need the appropriate 'Mini DigiLink to DigiLink' cables/adapters. Once again, 32 inputs/outputs will be available per Mini DigiLink connector from the rear of the Red 4Pre for a total of 64 I/O*.
*Please note that the Red 4Pre has 58 inputs and the final inputs after this number will not pass any audio.