The tool configuration on useGalaxy.org is fixed and cannot be modified. Alternatively, a local install or Cloudman instance can be modified to host any suite of tools from the toolshed using an account with administrative privileges.
To view an example instance of Galaxy with proteomics tools see the Galaxy-P public instance of Galaxy at https://usegalaxyp.org.
Hope this helps!
Thanks for using Galaxy!
Mo Heydarian, Galaxy Team