MassChroQ (Mass Chromatogram Quantification) is a free software (released under the Gnu General Public Licence version 3) for quantification of data obtained from Liquid Chromatography - Mass Spectrometry techniques.

MassChroQ performs alignment, XIC extraction, peak detection and quantification of LC-MS data. It is written in C++, has a Qt Graphical User Interface and is optimised for running smoothly on very large mzXML or mzML data on a desktop computer in a short time. It also offers paralelization for running in clusters and high performance computing facilities.

MassChroQ uses and produces only data in open standard formats (mxXML, mzML, gnumeric, csv etc.) It also accepts an on-purpose defined XML format called masschoqML, which offers the possibility of easily embedding MassChroQ's input or ouput in third party software. For example, MassChroQR is an R package processing masccroqML data for statistical analysis. Also, the X!Tandem pipeline's identified peptides can be automatically integrated into the masschroqML input file.

MassChroQ is available for download for several operating systems, including a Debian based package.

See the MassChroQ homepage for further documentation or the MassChroQ project on the SourceSup forge for development needs.

I worked with MassChroQ from 2009 until 2012, and I brought the project from a C++ home made prototype to its fully functional releasable state (releases 1.X until 2.0). During this period I was the main core developer, but I would have done nothing, not even a single thing, without the collaborative wonderful work of my development supervisor and mentor Olivier Langella, our team chief Michel Zivy and the naturally born hacker Benoit Valot. The project also benefited from the valuable help of our postdoctoral researchers Ludovic Bonhomme and Melisande Blein, who tested in real-time and pushed MassChroQ to its limits.