Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide
CHAPTER 7: Metabolomics Data Analysis Using MZmine
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Published:16 Mar 2020
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Special Collection: 2020 ebook collection
Tomáš Pluskal, Ansgar Korf, Aleksandr Smirnov, Robin Schmid, Timothy R. Fallon, Xiuxia Du, Jing-Ke Weng, 2020. "Metabolomics Data Analysis Using MZmine", Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide, Robert Winkler
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Rapid improvements in high-resolution mass spectrometry (HRMS) instrumentation since the early 2000s have led to equally dramatic developments in the fields of targeted and untargeted metabolomics.1 However, the MS instrument vendors initially lagged behind in software development, and the gap in raw MS data processing tools for metabolomics has been primarily filled by efforts from academia. The MZmine project was originally started in 2005 by Matej Orešic's group at VTT Biotechnology in Finland.2 It received a major overhaul towards modularity, spearheaded mainly by Tomáš Pluskal at the Okinawa Institute of Science and technology in Japan, and its second version, MZmine 2, was introduced in 2010.3 Since then, MZmine has grown into a worldwide collaborative project with many research labs and companies having contributed new code and data-processing modules. As of 2019, the project contains over 180 000 lines of Java source code. GitHub statistics indicate that the software has been downloaded over 56 000 times over the last four years, and our internal tracking system shows that over 4.3 million individual module runs have been performed in 2018 alone. In the last three years, MZmine has also been participating in the “Google Summer of Code” program, offering opportunities to computer science students to receive funding from Google for their contributions to the development of MZmine.4