Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 03/10/11
  • Minor correction: 08/11/11

masschroq : analysis and quantification of mass spectrometry data

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System: UNIX-like, Windows
  • Current version: 1.1 - September 2011
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Olivier Langella, Edlira Nano, Benoît Valot et Michel Zivy.
  • Contact designer(s):
  • Laboratory, service: PAPPSO


General software features

MassChroQ (Mass Chromatogram Quantification) is an open source software that performs quantification of mass spectrometry data, in paticular it has been designed to handle the analysis of proteomics data obtained from Liquid Chromatography - Mass Spectrometry (LC-MS) techniques. It can quantify a given list of mass over charge (m/z) values or all the identified peptides of your LC-MS data by performing retention time alignment, XIC extraction, peak detection and peak area quantification on them.

MassChroQ is very versatile: you can fully configure its parameters to best fit your data. You can quantify label-free data as well as isotopic labeled ones, data coming from low resolution spectrometers as well as high resolution ones, take into account complex data treatments as peptide or protein fractionation prior to LC-MS analysis (SCX, SDS-PAGE, ...) etc.
In addition, it is fast (takes less than 4 minutes to fully analyse 1Go of data), it is not greedy (uses at most 400 Mo of RAM at the time) and can perform automatical analysis of different groups of data samples in one shot.

MassChroQ uses and produces only open data formats : mzXML, mzML, gnumeric, csv and ods. It works by providing an input file in the masschroqML (XML) format, where the user indicates the data files to analyse (mzXML or mzML files) and the different analysis and corresponding parameters to perform on them. Sample masschroqML files are available online, you can edit and adapt them to your analysis. The identified peptides can be automatically filled in the masschroqML file in two ways: if you use X!Tandem as your identification engine, you can try the "X!Tandem pipeline" ( which performs peptide identification via X!Tandem, filtering and allows you to directly export the results in a masschroqML format. Otherwise, you can provide csv files containing the identified peptides (see the MassChroQ manual on how to do this).

MassChroQ is freely avalable under the GNU General Public Licence version 3 from

Context in which the software is used

MassChroQ is used in our proteomics research laboratory mainly to quantify the identified peptides of data analysed by LC-MS (Liquid Chromatography - Mass Spectrometry), with or without isotopic labelling, and sometimes with fractionation. The .raw data files coming directly from the spectrometers are first converted to mzXML or mzML formats. The peptides they contain are then identified (with the X!Tandem pipeline for example). Then the user edits a masschroqML file where he indicates the file path to the data to analyse together with the alignment, signal filtering and detection parameters he wants to use. Finally he launches MassChroQ on this file. Once MassChroQ has finished analysing the user can directly begin statistical processing on the output data. For more precise information a manual, a FAQ and various examples can be found on the software's homepage.

Publications related to the software