PaxDB 5.0: curated protein quantification data suggests adaptive proteome changes

Abstract

The "Protein Abundances Across Organisms" database (PaxDB) is an integrative meta-resource dedicated to protein abundance levels, in tissue-specific or whole-organism proteomes. PaxDB focuses on computing best-estimate abundances for proteins in normal/healthy contexts, and expresses abundance values for each protein in "parts per million" (ppm) in relation to all other protein molecules in the cell. The uniform data re-processing, quality scoring, and integrated orthology relations have made PaxDB one of the preferred tools for comparisons between individual datasets, tissues or organisms. In describing the latest version 5.0 of PaxDB, we particularly emphasise the data integration from various types of raw data, and how we expanded the number of organisms and tissue groups as well as the proteome coverage. The current collection of PaxDB includes 831 original datasets from 170 species, including 22 Archaea, 81 Bacteria and 67 Eukaryota. Apart from detailing the data update, we also show a comparative analysis of the human proteome subset of PaxDB against the two most widely-used human proteome data resources: Human Protein Atlas (HPA) and Genotype-Tissue Expression (GTEx). Lastly, we present a use case of PaxDB, showing how protein abundance data can be used to study the evolution of relative amino acid usage in Fungi.