We are formally at version 3. Older versions are archived on TeamCity.
There are several flavors of ProteoWizard depending upon your intended use. If you are primarily interested in using the tools, the binary distributions for your platform are most likely what you want. If you are interested in using ProteoWizard as part of a software project you are developing, you should get the source distribution, or check out the code from our GitHub repository directly. Other packages are also on Teamcity.
Developers interested in building ProteoWizard libraries for use in their own projects will note that there are a few choices for source distributions. Officially, the ProteoWizard libraries and tools are built using the bjam build system, but we also provide alternate semi-official build files for MSVC and for GNU/Autotools (the familiar old "configure ; make ; make install"). Note that these alternate build files do not support vendor DLLs: maintaining that capability is complex and thus limited to the officially supported bjam build. You can read more about it here.