MassChroQ was born in 2007 by Benoît Valot at the PAPPSO team while dealing with a great quantity of LC-MS data coming from different spectrometers. It first consisted of some perl scripts that analysed these data. But as the LC-MS data were becoming bigger and bigger, PAPPSO's bioinformaticist Olivier Langella, began writing in 2008 a C++ program called QuantiMScpp that already performed basic MS1 alignment, XIC-extraction, peak detection and quantification.

QuantiMScpp was used internally by the team members. In June of 2010 PAPPSO's computer engineer Edlira Nano joined the QuantiMScpp development adventure for a full time job on it. The software continued its development under the new name of MassChroQ and mature enough, on January, 2011 its first release version together with an academic article were published.

MassChroQ continues its development, new features and optimisation are continually being developed and released. Feel free to contribute to its development, or to simply suggest future features.