Comparative evaluation of in-depth mass spectrometry and Olink Explore 3072 for plasma proteome profiling

Recent advances in proteomics technologies have expanded the depth and scale of plasma proteome analyses, offering new opportunities for biomarker discovery and precision medicine. However, understanding the strengths and limitations of these technologies is crucial for study design and platform selection. We evaluated the performance and quantitative agreement of an in-depth mass spectrometry method (HiRIEF LC-MS/MS) and the Olink Explore 3072 proximity extension assay on 88 plasma samples, with 1,129 proteins analyzed with both methods. The technologies demonstrated complementary proteome coverage, high precision, and concordance in differential abundance analysis. Quantitative agreement in protein levels was moderate (median correlation 0.59, inter-quartile range 0.33–0.75), influenced by various technical factors. In addition, we introduce PeptOlink, a public resource for analyzing peptide-level quantitative agreement. Our findings highlight the complementary strengths of mass spectrometry proteomics and Olink Explore 3072, underscoring the value of combining both for comprehensive and reliable profiling of the plasma proteome.