Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues

The availability of an increasingly large amount of public
proteomics
data sets presents an opportunity for performing combined analyses
to generate comprehensive organism-wide protein expression maps across
different organisms and biological conditions. Sus
scrofa, a domestic pig, is a model organism relevant
for food production and for human biomedical research. Here, we reanalyzed
14 public proteomics data sets 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. Then, we studied how protein abundances
were compared across different data sets and studied the tissue specificity
of the detected proteins. Of particular interest, we conducted a comparative
analysis of protein expression between pig and human tissues, revealing
a high degree of correlation in protein expression among orthologs,
particularly in brain, kidney, heart, and liver samples. We have integrated
the protein expression results into the Expression Atlas resource
for easy access and visualization of the protein expression data individually
or alongside gene expression data.