Purpose:

This is a Docker image for running command-line ProteoWizard tools with vendor format support, which normally only work on Windows, on non-Windows platforms like MacOS and Linux. Tools like msconvert and SkylineCmd are included and you can see examples of using them below. If you don't know what Docker is or how to run things on a command-line, there will be a learning curve. See below for links to install and use Docker on MacOS and Linux.

Licensing:

In general, ProteoWizard is free for both commercial and non-commercial use, but you may not charge a fee for use of ProteoWizard (with vendor support enabled). And as the image name implies, you must agree to the vendor licenses to use this image. Read them here (switch between licenses at the top): http://proteowizard.sourceforge.net/licenses.html⁠

Installation:

• For MacOS, see here: https://docs.docker.com/desktop/install/mac-install/⁠
• For Linux, see here: https://docs.docker.com/engine/install/⁠
• For Windows, you don't need this container; you can just download a regular ProteoWizard⁠ installer.

Running:

This container provides only command-line tools. If you are not familiar with running things on the command-line, consider a tutorial such as this one⁠ for MacOS or this one⁠ for Linux. If you need a GUI interface to MSConvert or Skyline, you will need a real Windows machine or VM. Once you have a command-line open, see below for some example commands.

Examples:

In these examples, /your/data should be replaced with a local path on your host, such as /Users/johnsmith/my-mass-spec-data. The /data part is on the container side and you should not change it.

1. docker run -it --rm -v /your/data:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/file.raw -o /data
2. docker run -it --rm -v /your/data:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine SkylineCmd --dir=/data/Skyline-files --in=<input>.sky --import-file=<input>.raw --chromatogram-products --chromatogram-file=<output>.tsv

Supported vendor formats:

For msconvert command-line help:

docker run -it --rm proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert --help

For Skyline command-line help:

docker run -it --rm proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses wine SkylineCmd --help

Support:

If something goes wrong and there's no error, try rerunning with -e WINEDEBUG=fixme-all+msgbox+relay. If that doesn't help identify a solution, send your command-line and the output you get to support@proteowizard.org⁠. We may need a representative data file to test on as well.

This Docker image is built from the Dockerfile at: https://github.com/ProteoWizard/container⁠