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:

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.

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