I give MaxQuant and Perseus a tough time, and will probably continue to for the duration, despite the fact that -- if you can get them running and keep them running -- and are patient (for MaxQuant, I've never waited for Perseus to do anything, fast!) the data they produce is totally legit. How it gets there? Fuzzy on that, but this summer I added to my pile of Perseus installations that are labeled by what features work and don't work the ultimate prize -- uMAP, tSNE, and WGCNA
I gotta go and Docker is reminding me that the way they do free vs. nonfree changed in 2022 and I don't want to read all the things it says, so I can't run stuff through this one myself, but you can get MetaNetwork on Github here!