Running MaxQuant on Linux
There is a conda package for maxquant that should work on most platforms (I've used it on CentOS and I think it's been used on Ubuntu as well). There's also a docker container version of that that we (Bioconda) have posted to the biocontainers project that should also work.

Please note that large parts of a maxquant analysis are single threaded, regardless of what you specify. We've also had single analysis runs lasting over a month (even when using 90 threads), so the program can be very slow if your search space is large.