Integrated View of Baseline Protein Expression in Human Tissues

The availability of proteomics datasets in the public domain, and
in the PRIDE database, in particular, has increased dramatically in
recent years. This unprecedented large-scale availability of data
provides an opportunity for combined analyses of datasets to get organism-wide
protein abundance data in a consistent manner. We have reanalyzed
24 public proteomics datasets from healthy human individuals to assess
baseline protein abundance in 31 organs. We defined tissue as a distinct
functional or structural region within an organ. Overall, the aggregated
dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry
runs covering 498 samples from 489 individuals. We compared protein
abundances between different organs and studied the distribution of
proteins across these organs. We also compared the results with data
generated in analogous studies. Additionally, we performed gene ontology
and pathway-enrichment analyses to identify organ-specific enriched
biological processes and pathways. As a key point, we have integrated
the protein abundance results into the resource Expression Atlas,
where they can be accessed and visualized either individually or together
with gene expression data coming from transcriptomics datasets. We
believe this is a good mechanism to make proteomics data more accessible
for life scientists.