Msconvert Wine
From SPCTools
Proteowizard's msconvert utility is a must have tool for converting MS/MS data in almost any proprietary MS/MS data run into almost any of the commonly used open formats. While this tool is available on both Windows and Linux, the ability to convert many common formats under Linux is unavailable due to the need to have vendor specific libraries (dlls). Fortunately it *is* possible to run the Windows version of msconvert under Linux using Wine, a open source compatibility layer.
Instructions for Ubuntu
http://uec-images.ubuntu.com/releases/10.10/release/
Tested with 64 bit image ssh -X
sudo apt-get update sudo apt-get install wine sudo apt-get install cabextract wget http://www.kegel.com/wine/winetricks chmod 755 winetricks ./winetricks winxp ./winetricks vcrun2008 ./winetricks dotnet35
Download and install Proteowizard
Go to http://proteowizard.sourceforge.net/download.html using a web browser. Click on the artifacts link for the Windows x86 (or x86_64) build. When the TeamCity login page is displayed log in as guest using the link provided. Download the file with the tar.bz2 extension. Extract the package and move it to wherever you want to install it:
mkdir pwiz # cause pwiz is rude and pollutes cd pwiz tar xvf ../pwiz*.tar.bz2
