The data in this article are related to the research article entitled "Physiological comparability of the harmonized INFOGEST in vitro digestion method to in vivo pig digestion" (Egger et al., 2012). In this article, proteins identified in the different sections of pig skim milk powder (SMP) digestion are presented. In addition to the exemplary β-casein profiles of the paper, the peptide patterns of the other most abundant milk proteins during in vivo digestion in individual pigs are shown as heatmaps and line graphs. These data clearly reveal the digestion resistant protein regions and illustrate the variability between the pigs in the different sampling sections. Moreover, peptide patterns of the same SMP proteins comparing the harmonized in vitro digestion (IVD) with pig in vivo digestion show the physiological relevance of the IVD protocol. Finally, correlation coefficients were calculated to indicate similarities between pig sampling sections and gastric and intestinal IVD endpoints.