What is Proton? How does it work?
Proton is actually a few years older than the Steam Deck, which was first released in August 2018. At the time, Valve said that "Windows games with no Linux version currently available can now be installed and run directly from the Linux Steam client, complete with native Steamworks and OpenVR support."
Before Proton, gamers on Linux would often need native ports of games for their systems or be forced to rely on third-party compatibility layers such as Wine. Wine works quite well but often required a lot of tweaking to get things running perfectly, with games such as DOOM (2016) being playable with a bit of work.
Here's where Proton comes in. It removes the need for any work on the end user's side. The idea is that you can just install the game and play it as if it were a native port without the end user ever needing to know what's going on under the hood.
Proton works in conjunction with a modified version of Wine. Wine works as a layer translating Windows API calls to POSIX (Portable Operating System Interface) calls while also recreating a Windows directory structure and providing alternative implementations of system services. Wine doesn't use any emulation or virtualization to execute Windows binaries.
The other part of Proton that's essential to the gaming equation is its ability to translate Direct3D API calls. It includes DXVK, a Vulkan-based translation layer for Direct3D 9, 10, and 11, with support for Direct3D 12 provided via VKD3D-Proton, a fork of VKD3D from Wine.
As for Direct3D, it's a graphics API for Windows machines and is part of DirectX, and Proton essentially interprets these Direct3D API calls. Proton creates its own version of this library that games can interface with. Proton then internally routes these calls to the Vulkan API, allowing the game to run as if it were on a Windows machine.
Proton is entirely open source, which Valve says will "enable advanced users the ability to alter Proton." The most popular custom Proton build is Proton-GE, which incorporates the most recent Proton experimental changes. It contains other patches and features that regular Proton does not, as well.
The future of Proton
Proton can always be worked on and improved, but as it stands, it's already a mature and developed project. With massive titles already playable through it, there's not much more that gamers could ask for. There are still some compatibility problems and graphical glitches that crop up, but by and large, playing through Proton is indistinguishable from playing natively on Windows.
One thing that Valve could absolutely focus on next is to rebase the Wine version that Proton is based on to a more recent release. Proton lags behind the latest official Wine version by several releases, and open-source community projects such as Proton-GE aim to add additional features and rebase to more recent versions of Wine.
Of course, Valve's ultimate goal is stability and compatibility, which is why it doesn't just include all of these changes that projects such as Proton-GE have been able to achieve. If you're a power user then nothing is stopping you from installing and using Proton-GE instead, but for the everyday gamer, stable Proton is definitely the better option.