  Recently, many software tools have been developed to perform quantification
in LC-MS analyses. However, most of them are specific to either a
quantification strategy (e.g. label-free or isotopic labelling) or a
mass-spectrometry system (e.g. high or low resolution).
  In this context, we have developed MassChroQ, a versatile software that
performs LC-MS data alignment and peptide quantification by peak area
integration on extracted ion chromatograms. MassChroQ is suitable for
quantification with or without labelling and is not limited to high resolution
systems. Peptides of interest (for example all the identified peptides) can be
determined automatically or manually by providing targeted m/z and retention
time values. It can handle large experiments that include protein or peptide
fractionation (as SDS-PAGE, 2D-LC). It is fully configurable. Every processing
step is traceable, the produced data are in open standard format and its
modularity allows easy integration into proteomic pipelines. The output results
are ready for use in statistical analyses.
  Evaluation of MassChroQ on complex label-free data obtained from low and high
resolution mass spectrometers showed low CVs for technical reproducibility
(1.4%) and high coefficients of correlation to protein quantity (0.98).
  MassChroQ is freely available under the GNU General Public Licence v3.0 at
http://pappso.inra.fr/bioinfo/masschroq/.
