Documentation for Users

This page offers simple instructions for downloading and installing our ProteoWizard tools for people without programming experience. Many ProteoWizard tools use a command line. Following the installation instructions is a list of formats that ProteoWizard supports. Please visit our FAQ and Support pages if you have any questions.

Tools

In addition to providing libraries for creating new tools, the ProteoWizard project provides ready-made tools such as the popular MSConvert format conversion utility.

msConvert
chainsaw
msAccess
idConvert
msPicture
other ProteoWizard tools

Installation

Visit our Download page to get your desired version of ProteoWizard.

  • Windows Users: If you use the installer, then the only requirement is having Microsoft .NET Framework 4.0 or higher installed. To use the binary tarball distribution however, you must also have Visual C++ redistributables (for either x86 or x64 depending on which tarball you download) for these VC versions: 2008, 2010, 2012, 2013, 2015, 2017. This page links to the most recent redistributable for each VC version (NB: only get the redistributables, not the service packs). These are required because different vendor DLLs depend on different versions of VC.
  • Mac Users: You will need to unzip the ProteoWizard package, which will show up on your computer as a folder labeled pwiz and should end with .tar.bz2. In order to obtain the package, you will need to use either Stuffit-expander or Archive Utility (typically located in the Applications folder of your computer) to save and move the pwiz folder to your computer.
  • Linux Users: Navigate to the download directory. Once there, use 'tar xjvf [archive name].tar.bz2' on the archive and move the pwiz directory into a directory of your choice. PRO-TIP: For convenience, adjust your "PATH" environment variable to include your ProteoWizard tools directory, so that the command line tools may be run from any directory.

Supported Formats

  • Open Formats: ProteoWizard supports the reading/writing of the following open formats on all platforms (note: vendor formats require Windows with vendor libraries).

    • mzML 1.1
    • mzML 1.0
    • mzXML
    • MGF
    • MS2/CMS2/BMS2
    • mzIdentML
  • Proprietary Formats: ProteoWizard depends on vendor-supplied software libraries to access data in proprietary formats.

    Common Requirements You can check to see whether the required components are installed (Control Panel → Programs and Features).
    Vendor-Specific Requirements
    Accessing certain vendor-format data files requires an associated library, which has its own licensing terms. as indicated in the table below.

    Vendor Formats Vendor Required Software
    ABI T2D DataExplorer 4.0
    Agilent MassHunter .d distributed with ProteoWizard
    Bruker Compass .d, YEP, BAF, FID, TDF distributed with ProteoWizard
    Sciex WIFF / WIFF2 distributed with ProteoWizard
    Shimadzu LCD distributed with ProteoWizard
    Thermo Scientific RAW distributed with ProteoWizard
    Waters MassLynx .raw / UNIFI distributed with ProteoWizard
Website hosted by SourceForge.net. Fast, secure and Free Open Source software downloads