MZmine 2 is an open-source project delivering software for mass-spectrometry data processing, with the main focus on LC-MS data. It is an instrument that’s been developed with the help of the Java programming language. It is based on the original MZmine toolbox described in 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. It provides a user-friendly, flexible and easily extendable framework with a complete set of modules covering the entire LC-MS data analysis workflow.
Features
- Raw data file formats: MZmine 2 can read and process both unit mass resolution and exact mass resolution (e.g. FTMS) data in both continuous and centroided modes, including fragmentation (MSn) scans.
- Visualization: MZmine 2 can visualize your raw data together with peak picking and identification results, which is very useful for evaluating different peak detection methods.
- [advt]Peak picking: Peak detection in MZmine 2 is performed in a three-step manner: first, mass values are detected within each spectrum (several methods are available, depending on the nature of the data). In the second step, a chromatogram is constructed for each of the mass values which span over certain time range. Finally, deconvolution algorithms are applied to each chromatogram to recognize the actual chromatographic peaks.
- Peak list processing: There are several modules for further processing of peak detection results, including deisotoping, filtering and alignment. Identification of peaks can be performed by searching a custom database or by connecting to PubChem Compound database.
- Statistical analysis: MZmine 2 contains basic methods for statistical analysis of processed data. However, development of these methods is not considered high priority, as processed data can be easily exported to a third-party statistical software.
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