Raw data file formatsMZmine 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. Supported data formats are:
- mzML (mzML versions 1.0 and 1.1)
- mzXML (mzXML versions 2.0 to 3.1)
- mzData (mzData versions 1.04 and 1.05)
- NetCDF (no MSn support)
- Thermo RAW
- Waters RAW
Import and ExportIn order to exchange data with other applications, the following import and export file formats are supported:
- CASMI challenge task
- SQL database
Batch ProcessingMZmine 2 has the ability to run multiple data processing methods in batch mode using any of the methods available in MZmine. The batch mode can be run as a command-line application which makes it easy to integrate MZmine into automated data analysis workflows like QC systems.
Raw Data Methods
Filtering & SmoothingThere are several filtering and smoothing modules available for e.g. baseline correction, scan smoothing or cropping of the data.
Peak DetectionPeak detection 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 a certain time range. Finally, deconvolution algorithms are applied to each chromatogram to recognize the actual chromatographic peaks.
Peak List MethodsThere are several modules for processing of peaks lists, including:
- Gap Filling
- Isotope Detection
Identification of peaks can be performed by using any of the following:
- Custom database search
- Online database search (see below)
- Fragment or adduct search
Currently the following online databases are supported. Support for other databases may be implemented as additional plugins.