(Contributed by Jarrett Egertson)

MSConvert in a Linux Environment

  1. Download the windows build of proteowizard
    1. extract it: tar vxf pwiz-bin-windows-x86-vc90-1_6_1534.tar.bz2
    2. After extracting, msconvert.exe should be present
  2. Install and configure WINE

There are two ways to go about this: building from source or installing a binary, if you have a more common distribution (such as Ubuntu) installing a binary should work fine and be easier. If it's necessary to install from source, that's easy to do on a 32-bit system, but on a 64-bit system things get tricky....this page should help: http://wiki.winehq.org/WineOn64bit

  1. Install the cabextract linux package
    1. This package is required for step 4, a google search for ¿cabextract <your distribution name>¿ should suffice
  2. Use winetricks to set up the windows environment to work with msconvert
    1. Download winetricks from http://wiki.winehq.org/winetricks
    2. Install the vcrun2008 and dotnet20 tricks:
      1. sh winetricks vcrun2008 dotnet20
  3. Move the proteowizard libraries to the WINE environment
    1. The libaries are in the proteowizard archive, move all of the .dll files over to the WINE system_32 folder, on my system this was ~/.wine/drive_c/windows/system32
  4. Call msconvert.exe using WINE
    1. Change directories to where you extracted proteowizard and move msconvert.exe over to the WINE environment's program files directory (mv msconvert.exe ~/.wine/drive_c/Program\ Files)
    2. Call msconvert.exe using the follwing syntax wine "command"
      1. Example: wine "C:\Program Files\msconvert.exe data.RAW"


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