The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
A wonderful tool no doubt, but the project has left Linux users in the lurch. Version 4.8.0 has been a headache to install (see below *) and looking at 5.0.0, it looks like it's back to square one troubleshooting! (*) had to revert to gcc 4.8, which is not even available as package anymore in modern build, change "endform to end_form" in a perl module, changed paths in Proteowizard makefile, added "." to paths in Makefile, and quite a lot of the Apache config had to be adjusted !