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I think this book has something to do with Dungeons & Dragons, but the basic set up is that the Hadron Collider malfunctioned and all of the infinite universes (multiverse theory) converged and combined to create an apocalyptic world where all of these universes overlap.

The main girl has nanobots that can eat metal through her skin and she can shoot out like a gun, along with some other tricks that I can't fully remember. Her guardian/partner is this humanoid buffalo.

I think a "silver-surfer" type alien shows up near the middle or end but I am not certain.

As for when it came out, the only thing I can say is that it came out before 2012 for certain, and it must have been within 5 years of that, though I am not certain of that part. I say this because I first found it at my local library when in high school, and I remember it being a new adition to the library's catalogue at the time.

Probably Sooner Dead: A D&D Gamma World Novel (2011) by Mel Odom.

This Amazon review mentions the nanobots and the Hadron Collider:

Now it's been a long time since I cracked open a Gamma World rule book, so I forget what the mythology said about the cause of the apocalypse, but in these books it was a mishap with the Large Hadron Collider. It tore apart the world, and opened ripples, gateways to other worlds and dimensions, bringing all manner of strange creatures into ours.

Having the plot device of rampant inter-dimensional wormholes means that you can introduce basically anything you want into your story, and Mr Odom certainly took advantage of that. This book has human-animal hybrids, cyborgs, nanobot-enhanced humans, alien creatures, and more kinds of psionic abilities than I could count, all set in what 200 years before was known as Oklahoma.

The story follows Hella, a bio-engineered young woman with a mysterious past, and her bisonoid companion, Stampede, as they serve as guides for a group hunting for a lost object in the ruinous wastes of the American southwest. It's a fast-paced adventure chock full of gun fights, raiders, mutant creatures, mystery, loyalty, and betrayal.

Found with the Google query book "hadron collider" buffalo nanobots site:goodreads.com.