mineXpert2 is a free software package licensed under the GPLv3+ that helps you to visualize and explore MSⁿ mass spectrometric data.

The software was described in the following publication:

Langella O, Rusconi F. (2021) mineXpert2: Full-Depth Visualization and Exploration of MSn Mass Spectrometry Data. J. Am. Soc. Mass Spectrom., 4 (32) 1138-1141

Main Features

  • Highly detailed user manual in

  • Load any number of mass data files, either fully in memory or in streamed mode (when the files are larger than the available RAM);

  • A typical data exploration session would involve the following steps/actions:

    • Open a mass spectrometry file (the software automatically displays the TIC chromatogram). If the data are from an ion mobility-mass spectrometry (IM-MS) experiment, trigger an integration to a intensity=f(dt,m/z) color map. The TIC chromatogram and the color map can be used as starting points for the exploration of the data.

    • Perform a wide variety of integrations to a mass spectrum, a drift spectrum, a XIC chromatogram of color maps relating m/z with retention time, m/z with drift time or drift time with retention time. Each time an integration is performed, the obtained results are displayed in the corresponding window, either in a new plot widget or in an existing plot widget (depending on the user configuration for that integration). Each new plot (be it a TIC chromatogram, a mass spectrum, a drift spectrum or any kind of color map) can be the starting point of another integration to either the same kind of data or to any other kind of data. Various integrations in sequence allow the user to elaborate data exploration processes that drill each time farther into the depth of the data.

  • Each plot has specific functions associated to it: duplicate a trace plot, perform filtering or Gaussian fit, combine new integration results (either additively or subtractively), export as a (x,y) file, automatic recording of the relevant data of signalled peaks into a file using a predefined syntax.

  • A tabulated view of the whole mass data set in a given file allows one to filter the data according to a number of criteria that can be logically combined to craft hyper-stringent filtering operations(retention time, ion mobility, MS level, precursor ion m/z value, precursor ion charge, for example). Once the initial data set has been reduced to the desired mass spectra subset, the user may select the spectra perform tailored mass spectral data integrations to any of the trace or color map plots mentioned above.

  • Extremely flexible|powerful data views are available to allow sophisticated mass spectral data comparisons either from the same data set or from multiple data sets.

  • The IsoSpec module allows one to perform isotopic cluster calculations and to shape the obtained centroid values into Gaussian shapes that create the whole mass spectrum encompassing the various peaks of the isotopic cluster. The obtained mass spectrum can then be plotted in a plot widget like any other mass spectrum, which allows fine comparisons between experimental data and simulated data.

  • Available as Linux/Win10/macOS packages (see binary packages).