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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="author" content="Michael Doshi">
<title>ProteoWizard: Documentation</title>
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<h1>Documentation for Users</h1>
<!--<h2 id="subheading">A user's guide to ProteoWizard</h2>-->
<p>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 <a href="faq.html">FAQ</a> and <a href="support.html">Support</a> pages if you have any questions.</p>
<!-- TODO: Add Tutorials page -->
<!--<p>For tutorials on using ProteoWizard and its tools, visit the <a href="#">Tutorials</a> page under Documentation.</p>-->
<h2>Tools</h2>
<p>
In addition to providing libraries for creating new tools, the ProteoWizard project provides ready-made tools such as the popular MSConvert format conversion utility. <br><br>
<a href="tools/msconvert.html">msConvert</a> <br>
<a href="tools/chainsaw.html">chainsaw</a> <br>
<a href="tools/msaccess.html">msAccess</a> <br>
<a href="tools/idconvert.html">idConvert</a> <br>
<a href="tools/mspicture.html">msPicture</a> <br>
<a href="tools/tools_base.html">other ProteoWizard tools</a> <br>
</p>
<h2>Installation</h2>
<p>Visit our <a href="download.html">Download</a> page to get your desired version of ProteoWizard.</p>
<ul class="list-unstyled">
<li>
<span class="underline"><b>Windows Users</b></span>: If you use the installer, then the only requirement is having <a href="http://www.microsoft.com/download/en/details.aspx?id=17851">Microsoft .NET Framework 4.0</a> 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. <a href="https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads">This page</a> 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.
</li>
<li>
<span class="underline"><b>Mac Users</b></span>: 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.
</li>
<li>
<span class="underline"><b>Linux Users</b></span>: 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.
</li>
</ul>
<a id="SupportedFormats" class="heading">
<h2></a>Supported Formats</h2>
<ul class="list-unstyled">
<li>
<span class="underline"><b>Open Formats</b></span>: ProteoWizard supports the reading/writing of the following open formats on all platforms (note: vendor formats require Windows with vendor libraries).
<br>
<br>
<ul>
<li>mzML 1.1</li>
<li>mzML 1.0</li>
<li>mzXML</li>
<li>MGF</li>
<li>MS2/CMS2/BMS2</li>
<li>mzIdentML</li>
</ul>
</li>
<li>
<span class="underline"><b>Proprietary Formats</b></span>: ProteoWizard depends on vendor-supplied software libraries to access data in proprietary formats.
<br>
<br>
Common Requirements
<ul>
<li>Windows Vista, 7, 8, 10, 11</li>
<li><a href="http://www.microsoft.com/download/en/details.aspx?id=17851">Microsoft .NET Framework 4.8</a> or higher installed</li>
</ul>
You can check to see whether the required components are installed (Control Panel → Programs and Features).
<br>
Vendor-Specific Requirements
<br>
Accessing certain vendor-format data files requires an associated library, which has its own licensing terms. as indicated in the table below.
<br>
<br>
<table class="table">
<thead>
<tr>
<th>Vendor</th>
<th>Formats</th>
<th>Vendor Required Software</th>
<!--<th>License</th>-->
</tr>
</thead>
<tbody>
<tr>
<td>ABI</td>
<td>T2D</td>
<td>DataExplorer 4.0 (32-bit only)</td>
<!--<td><a href="../licenses/agilent.html">MHDAC</a></td>-->
</tr>
<tr>
<td>Agilent</td>
<td>MassHunter .d</td>
<td>distributed with ProteoWizard</td>
<!--<td><a href="../licenses/agilent.html">MHDAC</a></td>-->
</tr>
<tr>
<td>Bruker</td>
<td>Compass .d, YEP, BAF, FID, TDF, TSF</td>
<td>distributed with ProteoWizard</td>
<!--<td></td>-->
</tr>
<tr>
<td>Sciex</td>
<td>WIFF / WIFF2</td>
<td>distributed with ProteoWizard</td>
<!--<td><a href="../licenses/absciex.html">Wiff Reader Library</a></td>-->
</tr>
<tr>
<td>Shimadzu</td>
<td>LCD (except ITOF)</td>
<td>distributed with ProteoWizard</td>
<!--<td><a href="../licenses/"> </a></td>-->
</tr>
<tr>
<td>Thermo Scientific</td>
<td>RAW</td>
<td>distributed with ProteoWizard</td>
<!--<td><a href="../licenses/thermo.html" target="_blank">MSFileReader</a></td>-->
</tr>
<tr>
<td>Waters</td>
<td>MassLynx .raw / UNIFI</td>
<td>distributed with ProteoWizard</td>
<!--<td><a href="../licenses/waters.html">WRDAC</a></td>-->
</tr>
</tbody>
</table>
</li>
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<h3>Contribute</h3>
<p>Pull requests to our <a href="https://github.com/ProteoWizard/pwiz">GitHub repository</a> are always welcome! To get involved more formally, please email <a href="mailto:[email protected]" target="_top"><b>[email protected]</b></a></p>
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<p>3155 Porter Drive<br>Palo Alto, CA 94304</p>
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<h3>Donate</h3>
<p>If you would like to support the efforts of ProteoWizard, you can donate <a href="http://giving.stanford.edu/goto/mallickgift" target="_blank"><b>HERE</b></a>. Thank you so much for your support!</p>
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