Simple example to run Proton outside of Steam

run.sh

# Proton
# export PROTON_FORCE_LARGE_ADDRESS_AWARE=1 # just an example ignore this
export STEAM_COMPAT_DATA_PATH=~/Proton/half-life-3
export STEAM_COMPAT_CLIENT_INSTALL_PATH=~/.steam/steam
alias proton="~/.steam/steam/steamapps/Proton - Experimental/proton"

# Use Vulkan driver from Mesa instead of AMDVLK
export AMD_VULKAN_ICD=RADV

# Feral Gamemode
export LD_PRELOAD="$LD_PRELOAD:/usr/\$LIB/libgamemodeauto.so.0"

cd "~/Proton/half-life-3/pfx/drive_c/GOG Games/Half-Life 3" # Yes I got Half-Life 3 from GOG shut up

# Force Steam to use game's controller config
# Note 1 : change it back to appid 0 later after the game exits, you can do it in this script
#          but I don't wanna make this example too confusing. Maybe use a `;` at the end.
# Note 2 : Run steam with `steam -dev -console`, and run the non-Steam shortcut.
#          You can find the randomly generated appid for the shortcut in Steam's console.
# Note 3 : This is actually a bit slow to do, lol thanks steam
#steam steam://forceinputappid/3477727405

# gamescope
#gamescope -w 1920 -h 1080 -r 60 -U -- proton "hl3.exe"
# no gamescope
proton run "hl3.exe" 

Note: This does not run it with the Steam runtime. You can do that but I'm not covering that part.

Do not make bug reports, or expect support from the developers unless you're using the Steam runtime.
See this.