An 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 expression data in a consistent manner. We have reanalysed 25 public proteomics datasets from healthy human individuals, to assess baseline protein abundance in 32 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 68 healthy tissues, corresponding to 3,167 mass spectrometry runs covering 501 samples, coming from 492 individuals. We compared protein expression between the different organs, studied the distribution of proteins across organs, and identified proteins, as well as their isoforms, that are uniquely expressed in certain organs. We also 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 expression results into the resource Expression Atlas, where it can be accessed and visualised either individually or together with gene expression data coming from transcriptomics datasets.