Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling

The
plasma proteome is the ultimate target for biomarker discovery.
It stores an endless amount of information on the pathophysiological
status of a living organism, which is, however, still difficult to
comprehensively access. The high complexity of the plasma proteome
can be addressed by either a system-wide and unbiased tool such as
mass spectrometry (LC–MS/MS) or a highly sensitive targeted
immunoassay such as the proximity extension assay (PEA). To address
relevant differences and important shared characteristics, we tested
the performance of LC–MS/MS in the data-dependent and data-independent
acquisition modes and Olink PEA to measure circulating plasma proteins
in 173 human plasma samples from a Southern German population-based
cohort. We demonstrated the measurement of more than 300 proteins
with both LC–MS/MS approaches applied, mainly including high-abundance
plasma proteins. By the use of the PEA technology, we measured 728
plasma proteins, covering a broad dynamic range with high sensitivity
down to pg/mL concentrations. Then, we quantified 35 overlapping proteins
with all three analytical platforms, verifying the reproducibility
of data distributions, measurement correlation, and gender-based differential
expression. Our work highlights the limitations and the advantages
of both targeted and untargeted approaches and proves their complementary
strengths. We demonstrated a significant gain in proteome coverage
depth and subsequent biological insight by a combination of platformsa
promising approach for future biomarker and mechanistic studies.