Current Release

  • The latest release of MassChroQ is version 2.2.1 called "Black Caiman". This version brings natural isotope support to MassChroQ and a new matching algorithm. It requires less memory while computing faster. The natural isotope support brings more reliability to the results while decreasing the number of missing values.
  • The MassChroQ Studio is a graphical, user friendly tool, allowing the user to load mzml or masschroqML files and to perform XIC extraction, filtering, detection and alignment on them. The results of these operations can be instantly visualized on graphical plots. The goal of the Studio is to help the user to find the masschroqML parameters that best fit his/her data . The final parameters can be exported into masschroqML format, the user has only to integrate them in his masschroqML file.
  • The MassChroQ Guiis a simple graphical interface that allows the user to launch masschroq graphically, without having to do strange things on the command-line. Runtime messages of MassChroQ are displayed in a graphical console.

Previous Releases

  • The previous release version 2.1, called Yacare Caiman, was the first release to introduce multithread support. A lot of code refactoring was made to get better performances.
  • The previous release version 2.0, called Spectacled Caiman, was the first release to introduce MassChroQ GUI and MassChroQ Studio. The .time and .trace files: we have added the possibility for the user to decide whether he/she wants to load previous .time files or not, and if yes to indicate the directory where these files are. This way, one can use previous alignment results without having to repeat the alignment. When alignment is desired, the user has now to indicate the directory where the .time and .trace alignment files should be placed.
  • The previous release version 1.2, called Longteeth Crocklet, introduced peak post-matching feature, to match MS peaks that were not identified in the same run. In the previous versions, cross-run matching was based on the delta between the aligned RT of the detected peak to match and the aligned RT of the MS/MS that allowed identification in another run. Now, cross-run matching is based on the delta between the aligned RT of the peak to be matched and the aligned RT of the MS peak detected in the same run as the MS/MS that allowed identification. As the RT of the MS peak is more reproducible than the RT of MS/MS, matching is more precise.
  • The previous release version 1.1, called Speedy Crocklet, was much faster than the previous one (at most 3 minutes for 1 Go of fully analysed profile data), and much lighter (uses no more than 400 Mo of RAM) than the previous one.
  • The previous (and first) release version was 1.0 called "Hungry Crocklet".
  • Older unreleased versions can be found in the git repository.

Linux systems

Depending on your Linux system you can choose among two installation possibilities detailed below: from our Debian repository, or from source.
In all cases, the installation process installs a shared library called, 3 binary called masschroq, masschroq_gui & masschroq_studio, the masschroqml xsd schema and a manpage on your system. To check your installation you can type masschroq --help or man masschroq on a terminal.

Install for Ubuntu or Debian

Please follow repository installation instructions for Ubuntu, or Debian.
and then install it with synaptic or with the command :
sudo apt-get install masschroq masschroq-doc masschroq-studio masschroq-common masschroq-gui

Install from sources

MassChroQ version 2.2.1 Linux source files are available in this archive.
Decompress the archive and follow the instructions of the README file for compilation and install.


MassChroQ version 2.2.1 Windows 64-bit archive is available here.
Just extract archive on disk (you can use 7-zip), and use directly executable included. You must not remove .dll files.
Upgraded from older version : To ensure proper installation, you must first uninstall older MassChroQ installation before intall new ones.

Ready-to-use examples

Simple ready-to-use dataset examples are available in this archive.
They allow you to test your installation, but also to see and learn how MassChroQ works.
Furthermore, the masschroqML files of these examples are a good starting point in writing your masschroqML input file for your own MassChroQ analysis: just choose the one (or a combination of them) that better fits your analysis (labelling or not, high or low resolution), edit it and modify the LC-MS data and peptide file names/paths by making them point to your own data files. You can then launch MassChroQ with this masschroqML file. If syntax errors were introduced in this file during edition, MassChroQ will tell you the line/column numbers where the error was encountered.