Instructions to Download and Install ProteoWizard
We are working on a GUI to accompany our ProteoWizard tools. However, for the moment, the majority of ProteoWizard tools (except for msConvertGUI, Skyline, SeeMS, and Topograph) are command line.
To download ProteoWizard, you will:
1) Go to our download page [HERE]
2) Select the platform you would like to download
3) Read the Licensing Agreements
4) Click the 'I Agree to License Agreements, download ProteoWizard' button
Your browser will then download a tar.bz2 file containing ProteoWizard binaries (and source, if requested). ProteoWizard does not have a formal installer, except for Windows. Consequently, to install ProteoWizard, you have just to uncompress the downloaded archive (we recommend somewhere like c:\pwiz).
5) On windows, you will probably want to download the installer (if you downloaded the package instead, unzip the archive, which has a .tar.bz2 extension, using WinZIP into a directory of your choice. Many users alternately use 7-zip). You must have MSVC 2008 SP1 (x86), .NET Framework 3.5 SP1 and 4.0 installed: both versions are currently required for vendor DLL support.
5b) On macintosh, unzip the archive, which has a .tar.bz2 extension, using either stuffit-expander or Archive Utility on the archive and then moving the pwiz directory into a directory of your choice.
5c) On linux, navigate to the download directory and then use 'tar xjvf [archive name].tar.bz2' on the archive and them move the pwiz directory into a directory of your choice.
6) For convenience, adjust your "PATH" environment variable to include your ProteoWizard tools directory, so that the command line tools may be run from any directory.
On windows, the executable to convert data files is msconvert.exe or msConvertGui.exe. The installer will offer to add msConvertGui to your Windows Explorer menu. This allows you to right-click on a file or directory and open it in msConvertGui, with the default conversion parameters you deem appropriate for that kind of data. For instructions on how to use msconvert.exe from a command line, go to our tools page
Another way to look at the commands and options is to open a command window, navigate to the Proteowizard folder extracted in step 5, and type msconvert.exe without any options. Note that msconvert offers a few conversion filters that msConvertGui does not, newer filters tend to be added to msConvertGui later.