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.

Your attention, please

Bug fix in new version of ProteoWizard msconvert tool used to convert RAW files to mzML files I discovered that older versions of msconvert fail to correctly convert ion mobility mass spectrometry data. This bug was observed for Waters Synapt 2 files. Please, upgrade to the latest version of ProteoWizard software suite (I successfully tested version version 3.0.18271 downloaded today).

Test files are available

  • The downloads page contains two files that might be used for testing the program. These are ion mobility mass spectrometry data files.
  • The 20161027-cgb-wt-mobility.mzml mzML-formatted file has been obtained by converting a Waters Synapt G2 raw file using the msconvert tool of the ProteoWizard tool. The 20161027-cgb-wt-mobility.db 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.

Flash news

  • 2019 02 04 '''Release of version 5.8.1 (non-GNU/Linux)" A new version of msXpertSuite is made available with a more usable IsoSpec configuration procedure and even a more reliable element specification process. This new version is not available on GNU/Linux because the Debian repositories are frozen until the testing/stable switch.
  • 2019 01 31 '''Release of version 5.8.0 (non-GNU/Linux)" A new version of msXpertSuite is made available with a great new feature: isotopic cluster calculations based on the IsoSpec library. The new comprehensive feature is described in detail in the mineXpert user manual (see side bar). This new version is not available on GNU/Linux because the Debian repositories are frozen until the testing/stable switch.
  • 2018 10 14 User manual update! Completed the port of the user manuals from the LaTeX publishing system to the DocBook publishing system. DocBook allows one to format the document for print (PDF) or for online browsing (HTML). Please, see the User manual menu in the side bar.
  • 2018 10 14 Release of version 5.6.0 Any trace can now benefit from the Savitzky-Golay filter, with undo/redo. Easier creation of mass spectra on the basis of (x,y) data in the clipboard.
  • 2018 10 04 Release of version 5.5.3 Win7-10|MacOSX|GNU/Linux release. Improve the way the data file loader handles spurious pseudo-spectra in IM-MS data files obtained from Synapt2. Fix crash in the data slicer when the filename of the SQLite3 db file is not an absolute file path, that is, when the filename does not start at the root of the file system.
  • 2018 09 21 Release of version 5.5.2 Windows-7-and-10 and MacOSX only. For the Linux version of the software to be available in the Debian repositories, we wait for the QCustomPlot to be available in unstable (see older flash news item). This version fixes a few non-critical glitches in the 5.5.0/5.5.1 versions but keeps the following improvements:
    - mineXpert: Add new figures to the user manual and replace others. Update the user manual;
    - mineXpert: Provide a way for the user to configure the tolerance on the fractional part of the z value as is computed during deconvolution, document that new feature in the user manual;
    - mineXpert: Fix corner case crash when hitting Shift while right-button dragging in the colormap;
    - mineXpert: Improve GUI in the data slicer window;
    - mineXpert: When shift rescaling plots in multigraph plot widget, ensure the y axis full scale is determined on the basis of the greatest y value of all the graphs currently displayed in the view;
    - mineXpert: Allow changing the color of a TIC chrom plot right after data file loading (that is, even if it has no relations to other plots);
    - mineXpert: Replace TIC with XIC chromatogram text where needed;
    - mineXpert: Add computation of resolving power when mouse is moved over spectrum.
    • 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 09 14 Release of version 5.4.0 Windows-7-and-10 and MacOSX only: Port to the new QCustomPlot version 2.1. This was a long due port and is now done! There should be no visible differences to the user. Fixes to the mzML->SQLite3-based format converter in corner cases (Synapt HDMS 2 software). Improve single intensity value feedback to the user (in the console window, using the right color). For the Linux version of the software to be available in the Debian repositories, we wait for the QCustomPlot to be available in unstable (currently it is still in experimental).
  • 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.
  • 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