Background
Protein measurements from different affinity-proteomics platforms often correlate poorly, making interpretation of genetic and phenotypic associations challenging.
Findings
In 1930 participants across diverse ancestries, ~25–30% of associations were influenced by protein-altering variants, and 80 proteins showed ancestry-specific differences in correlations between platforms.
Conclusions
Adjusting for protein-altering variants improves inter-platform correlation and enables more accurate protein measurement across ancestries.