Msconvert Wine

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Proteowizard's msconvert utility is a must have tool for converting MS/MS data from almost any proprietary MS/MS data format into open standards formats (primary mzML and mzXML). While this tool runs 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) installed. Fortunately it *is* possible to run the Windows version of msconvert under Linux using Wine, a open source compatibility layer for Windows.

The following are instructions on how to install and setup Wine under a variety of Linux platforms. These instructions where largely derived from several spctools-discuss emails and a large thanks goes out to the users who posted this:

http://groups.google.com/group/spctools-discuss/browse_thread/thread/604745729ac0e541

http://groups.google.com/group/spctools-discuss/browse_thread/thread/bb2a608ad31f77dd/868fab027488bd09?hl=en&lnk=gst&q=wine#868fab027488bd09

http://groups.google.com/group/spctools-discuss/browse_thread/thread/2d98145b42479cb0/f8d80a25d1f8583c?hl=en&lnk=gst&q=wine#f8d80a25d1f8583c

1 Gotchas
2 Instructions for Ubuntu 64 bit
3 Instructions for CentOS 5.5
4 References

Gotchas

You will need to use wine in 32bit emulation mode. This is because .Net and Visual Studio libraries are required and these libraries are installed using a 32bit installer, even for the 64 bit versions of these libraries.

Instructions for Ubuntu 64 bit

The following instructions where tested on a Ubuntu Amazon Machine Image. See http://uec-images.ubuntu.com/releases/10.10/release/ for the image id.

Connect to the system you want to install on. If using ssh use the -X option to ensure display forwarding is set since parts of the setup will prompt you with GUI dialogs asking you to accept licenses.
ssh -X root@system
Update/install rpms
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 dotnet20
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:

cause pwiz is rude and pollutes the current directory
mkdir pwiz; tar xvf pwiz*.tar.bz2 -C pwiz

Note: you will get a click through license in a GUI dialog the first time you try to process any Agilent data

Instructions for CentOS 5.5

CentOS presents a bigger challenge, as you'll need the latest version of Wine and at the time these instructions where written there aren't pre-built rpms for it.

AMI: ami-01996f68

rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm

rpm -Uvh http://apt.sw.be/redhat/el5/en/x86_64/rpmforge/RPMS/rpmforge-release-0.5.2-2.el5.rf.x86_64.rpm

yum -y update

yum -y install xauth cabextract fontconfig gcc44 rpm-build

wget ftp://ftp.pbone.net/mirror/ftp.sourceforge.net/pub/sourceforge/h/project/hp/hphp/CentOS%205%2064bit/RPM/flex-2.5.35-7.x86_64.rpm

rpm -Uvh flex*

Log out, then log back in

CC=/usr/bin/gcc44 rpmbuild --define "_without_gstreamer 0" --nodeps

wget http://download.hostedgameservers.com/install-wine1.2.2.sh chmod 777 install-wine1.2.2.sh vi install-wine1.2.2.sh # remove the download, configure and make commands

rpm --nomd5 -ivh http://apt.sw.be/redhat/el5/en/source/wine-1.3.7-1.rft.src.rpm

ProteinProphet

MassLynx ./winetricks mfc42 wine regsvr32 DACServer.dll