msXpertSuite is Free Software licensed under the GNU General Public License version 3.

This means that you can use it freely for whatever need you may have, you may study the code underlying the program, you may modify that code freely and redistribute it freely with the same license as the one you got with the package.

For any comment, please use the maintainer address from here. Thank you.

French users:
the massXpert module of msXpertSuite is documented in a book about mass spectrometry for biochemists that I published. See for details.

All users:
The msXpertSuite youtube channel now provides video tutorials about the main aspects of the mineXpert software.

Flash news

  • 2018 06 21 Release of version 5.3.3 Improved loading of some ion mobility mass spectrometry (IM-MS) files from Agilent instruments (should not change anything for all the other situations).
  • 2018 06 06 Release of version 5.3.2 General review of all the JavaScript'ing developer documentation.
    • The downloads page contains two files that might be used for testing the program. These are ion mobility mass spectrometry data files.
      The mzML-formatted file has been obtained by converting a Waters Synapt G2 raw file using the msconvert tool of the ProteoWizard tool. The db-formatted file has been obtained by converting the previous mzML-formatted file to a private (yet open) SQLite3-based db format that is much more speedy in terms of data load).
    • New video tutorials are available on YouTube. The video tutorials describe the features of the program and are conveniently organized in a playlist that affords a progressive introduction to the mineXpert software complexity.
  • 2018 05 31 Release of version 5.3.0 Ensure that operations are perfectly sequential during the JavaScript'ing of mineXpert.
  • 2018 05 29 Release of version 5.2.1 Fix small glitch with a helper message string about integrations to XIC chromatograms from the Drift spectrum window.
  • 2018 05 25 Release of version 5.2.0 Fix mzML to SQLite3 db format conversion on MS Windows.
  • 2018 05 24 Release of version 5.1.1 Major release! All the blocking computations (mainly integrations) are now handled in their own processing thread, which yields a totally fluid user interface even when extremely heavy computations are being carried over. Lost of refinements and bug fixes.
  • 2018 04 24 Release of version 5.0.2 Bug fix release. Fix bug with the failing charge state envelope deconvolution of mass spectra.
  • 2018 04 17 Release of version 5.0.0 This is a milestone release, with many bug fixes and new features, like almost pervasive scriptability using JavaScript, very much improved mathematics when spectrum combination is at work (handling the vast diversity of mass data from various instruments/vendors), Savitzky-Golay filtering of mass spectra... Finally the documentation has been thoroughly updated and now documents every aspect of the mineXpert software.
  • 2018 01 16 Release of version 4.2.0 that is a Mac OS X-only release that fixes the problem with failed install on Mac systems older than the latest version. Now the bundles should install successfully on older systems, up to 10.9.0. Please, send your feedback here. The download of the Mac package: here.
  • 2018 01 05 Release of version 4.1.0. Check the Downloads. The Debian packages have now entered the sid and testing distribution. The MS-Windows package now only is for the amd64 platform. First working MacOSX package available! Please, test it and report! Also, head to Debian GitLab instance to check out the code.
  • 2017 10 17 Release of version 3.7.0. Check the Downloads. The Debian packages have now entered the sid and testing distribution. The MS-Windows package now only is for the amd64 platform. I am currently pondering the possibility to resurrect the MacOSX packaging.
  • 2017 07 17 Release of version 3.6.3. Check the Downloads. At the moment, only the source tarball and the MSWindows installer are available. The Debian packages are in the NEW queue and should be available in the servers in some days. Later on, they will automatically be on the Ubuntu servers and all Debian- or Ubuntu-derived distributions.
  • 2017 07 09 New website for the brand new msXpertSuite mass spectrometry package. The massXpert project has now become a module inside the msXpertSuite project.
  • When using the massXpert module of msXpertSuite, please do still cite the publication. The mineXpert module is not yet described in a publication.

msXpertSuite is about mass spectrometry.

This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system. With msXpertSuite you actually have two modules:

1. massXpert sports four sub-modules:

  • With the XpertDef module you define brand new polymer chemistries (what are the atoms (isotope/abundance pairs), what are the monomers that make the polymer, what are the chemical modifications that you might need to simulate biological or synthetic chemical reactions, what are the different ways you might need to cut a polymer sequence into pieces (chemical or enzymatic), what are the different ways that a small oligomer might fragment in the mass spectrometer's gas phase, and so on...
  • With the XpertCalc module, you get a desktop calculator that understands your polymer chemistry definitions as defined in XpertDef. The calculator allows any kind of chemical reaction and is infinitely programmable. Any calculation is recorded in a logbook that is exportable to put in the lab-book;
  • With the XpertEdit module, you get a sophisticated polymer sequence editor and a chemical center where a huge amount of simulations might be performed. Anything mass-related is virtually feasible in XpertEdit.
  • With the XpertMiner module, you have a data mining center. You can drag and drop data from the mass spectra (in the form of m/z lists) and data from the simulations performed in the XpertEdit module. Once there, all the data will be available for comparison, arbitrary calculations like, say : "this list of m/z values should be applied the following mass increase" or "this list of m/z values should be appplied this reaction: -H+Na". The possibilities are infinite.

2. mineXpert (features) can be used to load mass spectrometry data files and show the spectral data in a plot widget for further analysis according to a variety of available integrations. While this program can operate integrally in a graphical mode, it is also widely scriptable using JavaScript as a scripting language. 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 or a drift spectrum) is potentially the start of another integration. 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, slicing of the data file into smaller data files.
  • One feature of importance is the fact that a large part of the functionalities of the program are scriptable (JavaScript) and a powerful scripting console is available to elaborate scripts before storing them in script files to be automatically executed.

Flying frog image courtesy of