Proteomics has gained a wide interest in the last decade since it involves the comparative study of protein expressions to identify bio-markers for early diagnosis of unpredictable, and serious, pathologies. The most powerful techniques for protein investigation compare 2D gel electrophoresys images that represent the protein composition of healthy and diseased tissues. Nevertheless, this analysis is problematic since gel images are affected by high noise levels and they are distorted, so that the same protein spot has different locations on different gels. Furthermore, the acquisition of a statistically significant sample of gels from a unique laboratory is problematic due to ethical problems, to the rarity of certain diseases, and to the fact that the process of gel electrophoresys is time consuming and costly. However, a great deal of information is present in the scientific literature in the form of images reporting 2D gels acquired for different experiments, we have developed a framework to compare annotated 2D gel images extracted from state of the art, and publicly available papers. The system has been assessed by performing the comparative analysis of the Haptoglobin; although the analyzed images are much more noisy and distorted than their sources the system achieves promising results.