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faq.html
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<!DOCTYPE html>
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<meta name="author" content="Michael Doshi">
<title>ProteoWizard: FAQ</title>
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<h1>FAQ</h1>
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<p>Here is a compilation of the most frequently asked questions we have received. Click on a question to see its answer. Don't see your particular question? Check out our <a href="support.html">support</a> page to find out where to direct your question, so we can best answer it.</p>
<details>
<summary><b>What is ProteoWizard?</b></summary>
<p>ProteoWizard is a set of tools and libraries to facilitate proteomics data analysis and to facilitate developing applications for proteomics data analysis.</p>
</details>
<details>
<summary><b>How do I cite ProteoWizard?</b></summary>
<p>
If you use or incorporate the ProteoWizard tools or libraries, please cite our Nature Biotechnology Commentary
<br>
<br>
A cross-platform toolkit for mass spectrometry and proteomics. Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. Nature Biotechnology 30, 918-920 (2012). <a href="http://www.nature.com/nbt/journal/v30/n10/full/nbt.2377.html"><b>Article →</b></a>
<br>
<br>
and/or Our Bioinformatics Application Note [<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn323?ijkey=BNjsLHD6Ki2zYgS&keytype=ref" target="_blank">abstract</a>] [<a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn323?ijkey=BNjsLHD6Ki2zYgS&keytype=ref" target="_blank">pdf</a>]
<br>
<br>
ProteoWizard: Open Source Software for Rapid Proteomics Tools Development
<br>
Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick
<br>
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323
</p>
</details>
<details>
<summary><b>What is the current status of ProteoWizard?</b></summary>
<p>We have released version 3.x of the library, together with a set of command line tools. Binary packages are only available for download from our <a href="download.html">download</a> page, but source code is available both there and at our <a href="https://github.com/ProteoWizard/pwiz" target="_blank">GitHub project</a></p>
</details>
<details>
<summary><b>What formats does ProteoWizard support?</b></summary>
<p>
On all platforms: mzML (1.1 and 1.0), mzXML, mz5, MGF, MS1/MS2, mzIdentML, and traML
<br>
<br>
On Windows, with vendor libraries: Agilent, Bruker, Sciex, Shimadzu, Thermo, and UIMF.
</p>
</details>
<details>
<summary><b>Who is using ProteoWizard?</b></summary>
<p>
Hundreds of labs around the world are using different ProteoWizard tools. The central developers are at the Center for Applied Molecular Medicine (CAMM) at the University of Southern California, the Canary Center for Early Detection at Stanford University, the Vanderbilt University Mass Spectrometry Research Center and at the MacCoss lab at the University of Washington, Seattle. Each of these groups use ProteoWizard extensively in daily data analysis.
<br>
<br>
The ProteoWizard libraries are also being used by the Trans-Proteomic Pipeline (TPP) and the Computational Proteomics Analysis System (CPAS) tools for mzML support.
</p>
</details>
<details>
<summary><b>I want to contribute!</b></summary>
<p>Great! We are happy to review Pull Requests to our <a href="https://github.com/ProteoWizard/pwiz">GitHub repository</a>.</p>
</details>
<details>
<summary><b>Where is your source code repository?</b></summary>
<p>In 2018, we migrated from SourceForge to <a href="https://github.com/ProteoWizard/pwiz">GitHub</a> (and from SVN to Git).</p>
</details>
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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>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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