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MZmine 2 is an open-source project delivering a software for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable framework with a complete set of modules covering the entire LC-MS data analysis workflow.

MZmine project was initiated by Matej Oreši? of Quantitative Biology and Bioinformatics group at VTT Technical Research Centre of Finland and Mikko Katajamaa of Computational Systems Biology Research group at Turku Centre for Biotechnology in 2004. First release in 2005 introduced the data processing workflow and implemented simple methods for each data processing task and data visualization.

The project entered a second phase as Tomáš Pluskal of G0 Cell Unit at Okinawa Institute of Science and Technology joined the project in 2006 and started a process of redesigning the software framework towards modularity. A paper about MZmine 2 was published in BMC Bioinformatics in 2010.