Abstract: The present invention relates to an improved method for comparing two or more samples containing proteins. This invention consists in first correlating and selecting the huge amount of data generated by mass spectrometry (PMF and MS/MS) before any kind of protein identification process, and then only identifying the proteins that are differentially expressed in dissimilar proteomes and thus have a potentially important biological interest. To do so, the experimental data resulting from separation and mass spectrometry are first correlated according to a correlation method, and then selected according to specific selection criteria. At this stage only, the selected data are analysed to identify the corresponding proteins.