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<!DOCTYPE html>
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<h2>MZmine</h2>
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<h2 style="display: inline-block;">About <strong>MZmine 3</strong></h2>
<span style="float:right;"><a class="btn btn-primary" href="https://github.com/mzmine/mzmine3/releases/latest">Download</a> <a class="btn btn-primary" href="https://mzmine.github.io/mzmine_documentation/">Documentation</a> <a class="btn btn-danger" href="https://github.com/mzmine/mzmine3/issues">Report issue</a></span><br/>
MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in the <a href="https://academic.oup.com/bioinformatics/article/22/5/634/206500">2006 Bioinformatics publication</a>, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire LC-MS data analysis workflow.
<br/><br/>
If you are interested in implementing your own data processing methods or help improve MZmine 3 then please check the <a href="development.html">development page</a>.
<br/><br/>
Please cite the following publication if you use MZmine to analyze your data:<br/>
<i>Schmid, R., Heuckeroth, S., Korf, A. et al.</i> Integrative analysis of multimodal mass spectrometry data in MZmine 3.
Nature Biotechnology (2023). <a href="https://doi.org/10.1038/s41587-023-01690-2">https://doi.org/10.1038/s41587-023-01690-2</a>
<br/><br/>
The MZmine 2 publication is also a relevant resource:
<i>T. Pluskal, S. Castillo, A. Villar-Briones, M. Orešič, MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics 11:395 (2010). <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=MZmine+2%3A+Modular+framework+for+processing%2C+visualizing%2C+and+analyzing+mass+spectrometry-based+molecular+profile+data" target="_blank">PMID: 20650010</a></i>
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<h2>Project <strong>History</strong></h2>
MZmine was initiated by Matej Orešič (<a href="http://www.vtt.fi/" target="_blank">VTT Technical Research Centre of Finland</a>) and Mikko Katajamaa (<a href="http://www.btk.fi/" target="_blank">Turku Centre for Biotechnology</a>) in 2004. The first version, <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btk039v1" target="_blank">MZmine 1</a>, was published in 2005 and introduced the data processing workflow and implemented simple methods for data processing and visualization.
<br/><br/>
The project entered the second phase in 2006 when Tomáš Pluskal (<a href="http://www.oist.jp/" target="_blank">Okinawa Institute of Science and Technology</a>) joined the project and redesigned the software framework towards modularity. <a href="http://www.biomedcentral.com/1471-2105/11/395" target="_blank">MZmine 2</a> was published in 2010.
<!-- <br/><br/>
In 2015, the project entered the third phase with the initiation of the <a href="https://msdk.github.io/" target="_blank">Mass Spectrometry Development Kit (MSDK)</a> by Tomáš Pluskal. The goals of MSDK is to integrate the existing algorithms that are scattered around in various Java-based mass spectrometry software. This will then be the new framework on which MZmine 3 will be developed. -->
<br/><br/>
In 2022, MZmine 3 builds on the success of MZmine 2 with many features focused on improving the user-friendly graphical user interfaces and performance in data processing of thousands of mass spectrometry data files. The development was mainly organized between Robin Schmid (<a href="https://dorresteinlab.ucsd.edu/" target="_blank">University of California San Diego</a>), Steffen Heuckeroth (<a href="https://www.uni-muenster.de/Chemie.ac/en/hayen/index.html" target="_blank">University of Münster</a>), Ansgar Korf (<a href="https://www.uni-muenster.de/Chemie.ac/en/karst/index.html" target="_blank">University of Münster</a>), and Tomáš Pluskal (<a href="https://pluskal.group.uochb.cz/en" target="_blank">Institute of Organic Chemistry and Biochemistry</a>)
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