About massXpert

massXpert 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 : massXpert is documented in a book about mass spectrometry for biochemists that I published.'
See http://www.lavoisier.fr for details.

Flash news

I cannot prepare MacOSX packages anymore as I have no more a MacOSX computer at my disposal. If anyone wants to donate a Mac computer, I'll resume package creation. Thank you.

  • 2016 04 18 The main massXpert website is no more using the massxpert.org domain name. We were hosted by TuxFamily.org before and we were using Gandi.net for the massxpert.org domain name purchasing. But we were rather unsatisfied with Gandi.net, particularly their bad communication with customers, specifically knowing that I am a Debian Developer. So we decided not to renew the massxpert.org domain name. We are immensely grateful to the TuxFamily.org people for their first-class web site hosting service. So, now, massXpert is located at massxpert.tuxfamily.org.

  • 2015 09 20 New release, version 3.6.0. This release introduces a major change in the way fragmentation calculations are performed. In prior versions, the fragmentation specifications implicitely yielded fragment ions in the default ionization form of the corresponding polymer chemistry definition. For example, fragmented peptides produced product ions that were protonated by default. Likewise, fragmented oligonucleotides produced product ions that were deprotonated by default. This way of computation fragmentations turned out to be a limitation when one desired to compute fragmentations in the opposite ionization mode with respect to the default ionization mode described in the polymer chemistry definition (for example negative ionization mode fragmentation of peptides). Now, the fragmentation specifications need to yield neutral molecular species, which then undergo ionization according to the ionization currently being used in the XpertEdit module, that might be different than the one described as the default ionization mode of the corresponding polymer chemistry definition. This way of doing is much more flexible and usable than the older way of doing things. So, please, ensure that all your polymer chemistry definitions are updated according the new way of calculating fragments. The dna/saccharide and protein chemistry definitions have been updated in the distribution.

  • 2012 12 25 New release, version 3.4.0.

  • 2011 10 22 New release, version 3.2.0.

Update: Debian GNU/Linux users: a debugging symbols package will be available soon, as package massxpert-dbg;

  • 2011 06 05 Performed my first debian package upload as a Debian Developer !

  • The packages for MS-Windows and MacOSX no more ship the user manual. Please download it from the website.

  • Publication of massXpert in the prestigious british journal Bioinformatics, UK. See News (Section July)!

massXpert 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 massXpert you actually have four programs in one :

  1. With the XpertDef module you define brand new polymer chemistries (what are the atoms, 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...

  2. 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;

  3. 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.

  4. With the XpertMiner module, you will get (it is being implemented) a data mining center. You'll be able to 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 should be infinite.