Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

Proteotypes, like genotypes, have been found to vary between individuals in several studies, but consistent molecular functional traits across studies remain to be quantified. In a meta-analysis of 11 proteomics datasets from humans and mice, we use co-variation of proteins in known functional modules across datasets and individuals to obtain a consensus landscape of proteotype variation. We find that individuals differ considerably in both protein complex abundances and stoichiometry. We disentangle genetic and environmental factors impacting these metrics, with genetic sex and specific diets together explaining 13.5% and 11.6% of the observed variation of complex abundance and stoichiometry, respectively. Sex-specific differences, for example, include various proteins and complexes, where the respective genes are not located on sex-specific chromosomes. Diet-specific differences, added to the individual genetic backgrounds, might become a starting point for personalized proteotype modulation toward desired features. [Display omitted] •Benchmarking of datasets on human and mouse proteotypes•Consistent co-variation landscape of functional modules across individuals•Protein complexes vary in their stoichiometry across individuals•Quantifying effects of genetic sex and specific diets on complexes Protein functional module variation between individuals might serve as molecular fingerprints for a wide range of environmental and genetic factors that are tunable by intervention toward desired proteotypes.