Integrated analysis of baseline protein expression in pig tissues

Abstract

AbstractThe availability of an increasingly large amount of public proteomics datasets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions.Sus scrofa, the domestic pig, is a model organism relevant for food production and for human biomedical research. Here we reanalyzed 14 public proteomics datasets from the PRIDE database coming from pig tissues to assess baseline (without any biological perturbation) protein abundance in 14 organs, encompassing a total of 20 healthy tissues from 128 samples. The analysis involved the quantification of protein abundance in 599 mass spectrometry runs.We compared protein expression patterns among different pig organs and examined the distribution of proteins across these organs. The number of canonical proteins per dataset ranged from 789 (dataset PXD002918, biceps femoris) to 6,062 (dataset PXD012636, heart). Then, we studied how protein abundances compared across different datasets. Of particular interest, we conducted a comparative analysis of protein expression between pig and human tissues (from a previous study performed following the same methodology), revealing a high degree of correlation in protein expression among orthologs, particularly in brain, kidney, heart, and liver samples. Additionally, we analysed the differences in quantitative expression of proteins across organs between human and pig organs.We have integrated the protein expression results into the Expression Atlas resource for easy access and visualisation of the protein expression data individually or alongside gene expression data.