General 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. 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 Export

In order to exchange data with other applications, the following import and export file formats are supported:

  • CASMI challenge task
  • mzTab
  • XML
  • CSV
  • MetaboAnalyst
  • mzTab
  • SQL database
  • XML

Batch Processing

MZmine 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 & Smoothing

There are several filtering and smoothing modules available for e.g. baseline correction, scan smoothing or cropping of the data.

Peak Detection

Peak 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 Methods

There are several modules for processing of peaks lists, including:
  • Gap Filling
  • Isotope Detection
  • Filtering
  • Alignment
  • Normalization
  • Identification

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.

Statistical Analysis

MZmine 2 contains basic methods for statistical analysis of processed data. Processed data can also easily be exported to third-party statistical software for advanced analysis.

Data Visualization

MZmine 2 can visualize your raw data together with peak picking and identification results. This is very useful for evaluating different peak detection methods and getting an overview of the data. Plots can be exported to vector graphics for high quality printing.