Full disclosure, I haven't tried the PhosphoDisco yet, but I'm always on the hunt for the elusive package where I can put in phosphoproteomic data and the program will help it make sense.
Is the PhosphoDisco it? Maybe? The Broad makes tools great enough that they can make sense of SpectrumMill data, so I'm cautiously optimistic and I'll leave the manuscript here.
What you might actually want is this Github link, though, where the documentation is!