Correlations Within and Between Highly Multiplexed Proteomic Assays of Human Plasma

Abstract

Introduction: The number of assays on proteomic platforms has grown rapidly. The leading platforms, SomaScan and Olink, have strengths and limitations. Comparisons of precision on the latest platforms-SomaScan 11k and Olink Explore HT-have not yet been established.

Methods: Among 102 participants in the Atherosclerosis Risk in Communities Study (mean age 74 years, 53% women, 47% Black), we used split plasma samples to measure platform precision. CV and Spearman correlations were calculated for each assay. Cross-platform agreement was assessed for overlapping proteins.

Results: SomaScan 11k demonstrated a median correlation of 0.85 for the 10 778 assays and a median CV of 6.8%, similar precision to earlier versions. The 5420 assays on Olink Explore HT exhibited a median correlation of 0.65 and median CV of 35.7%, which was higher than observed in its predecessors (e.g., 19.8% for Olink Explore 3072). Precision of Olink assays was inversely correlated with the percentage of samples above the limit of detection (LOD) (r = -0.77). Upon replacing Olink values below the LOD with values half the LOD, the median correlation for Olink assays measured in duplicate increased to 0.79; the median CV decreased to 13.3%. The distribution of between-platform correlations for the 4443 overlapping proteins had peaks at r approximately 0 and at r approximately 0.8. One-tenth of the protein pairs had cross-platform correlations r ≥ 0.8.

Conclusions: Precision of these 2 proteomics platforms in human plasma has diverged as the coverage has increased. These results highlight the need for careful consideration in platform selection based on specific research requirements.