This is a semi-official ProteoWizard build system that uses GNU autotools instead of bjam.
It leaves out support for vendor formats and MZ5 due to their extra build complexity.
If you need those, you'll want to learn the bjam system (and you'll need to be on windows, for vendor DLLs).
To use this GNU autotools build, from the pwiz directory just run:
Have a look at the autotools/README file if this does not go smoothly.
Please visit http://proteowizard.sourceforge.net for the full official bjam build system, or to obtain updates to this GNU build system.