Part of our work aims at studying the modifications that proteins suffer in foods and use them as markers to estimate the origin and history of the product. Proteomics is a powerful approach to do this: comparison of the two-dimensional (2-D) maps of the intact and treated samples would permit to identify marker spots so that in the future it may be possible to estimate the treatment a foodstuff has suffered by examining its 2-D protein map or just the selected markers. This work summarizes some of our previous studies showing the application of proteomics to the (i) identification of species and muscle tissues, (ii) characterization of post-mortem changes in arctic and tropical species, and (iii) study of the effect of some additives during the processing of fish muscle.