Application of iTRAQ to catalogue the skeletal muscle proteome in pigs and assessment of effects of gender and diet dephytinization.

In this study iTRAQ was used to produce a highly confident catalogue of 542 proteins identified in porcine muscle (false positive<5%). To our knowledge this is the largest reported set of skeletal muscle proteins in livestock. Comparison with human muscle proteome demonstrated a low level of false positives with 83% of the proteins common to both proteomes. In addition, for the first time we assess variations in the muscle proteome caused by sexually dimorphic gene expression and diet dephytinization. Preliminary analysis identified 19 skeletal muscle proteins differentially expressed between male and female pigs (> or = 1.2-fold, p<0.05), but only one of them, GDP-dissociation inhibitor 1, was significant (p<0.05) after false discovery rate correction. Diet dephytinization affected expression of 20 proteins (p<0.05). This study would contribute to an evaluation of the suitability of the pig as a model to study human gender-related differences in gene expression. Transgenic pigs used in this study might also serve as a useful model to understand changes in human physiology resulting from diet dephytinization.

Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines.

Porcine liver proteome iTRAQ analysis enabled the confident identification of 880 proteins with a rate of false positive identifications of less than 5%. Proteins involved in energy metabolism, catabolism, protein biosynthesis, electron transport, and other oxidoreductase reactions were highly enriched confirming the central role of liver as the major chemical and energy factory. Comparative analysis with human and mouse liver proteomes demonstrated that 80% of proteins were common to all three liver proteomes. In addition, it was also demonstrated that both sex of the animal and introduction of a novel phytase transgene into the genome each affected around 5% of total liver proteome. After controlling the false discovery rate (FDR