mineXpert2 is part of the msXpertSuite software package.

mineXpert2 is a full rewrite of the first mineXpert software published in 2019 in ACS Journal of Proteome Research.


  • 2020 07 24 Version 6.0.2
    Fix: the program still accessed the user manual from the previous version.

This is a comparison of the software versions:

  • mineXpert2 is now coded with true execution parallelism, delivering much better calculation performance and user experience (no window lock-ups when intensive tasks are performed);
  • mineXpert2 is MSn-capable, while mineXpert was MS1-only;
  • mineXpert2 now features more mass spectral integration types, like color map views not available in mineXpert;
  • mineXpert2 has a very much improved data window management with lots of new features that aid in the mass spectrometric data comparisons across samples.

If you use this program, please cite it using this reference:

Filippo Rusconi (2019) mineXpert: Biological Mass Spectrometry Data Visualization and Mining with Full JavaScript Ability. Journal of Proteome Research, 18 (5), 2254-2259. DOI: 10.1021/acs.jproteome.9b00099

Video screen captures showcasing mineXpert2 features here.

To download the software, please check the Downloads menu on the side bar.

mineXpert2 has the following major features:

  • 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 mining session would involve the following steps/actions:
    - Open a mass spectrometry file and immediately compute a TIC chromatogram, show that chromatogram in a dedicated window. If the data are from an ion mobility mass spectrometry (IM-MS) experiment, compute a mz=f(dt) color map. The TIC chromatogram and the color map are then the starting points for the mining of the data.
    - Perform a wide variety of integrations to a mass spectrum or a drift spectrum. Each new spectrum is displayed in its dedicated window (the TIC chromatogram window, the Color map window, the Mass spectrum window and the Drift spectrum window). 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 view or to any other kind of data view. Various integrations in sequence allow the user to elaborate data mining processes that drill each time farther in the depth of the data.
  • Each plot has specific functions associated to it: export as a (x,y) file, automatic recording of the relevant data of signalled peaks into a file using a specific easy-to-understand grammar.
  • A tabulated view of the whole set of mass spectra in a given file allows one to filter the data according to a number of parameters (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, the user may select them and use them to compute tailored mass spectral data integrations.
  • 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.