Multi-platforms approach for plasma proteomics: complementarity of Olink PEA technology to mass spectrometry-based protein profiling

Abstract

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 structural 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 Assays (PEA). In order to address relevant differences and important shared characteristics, we tested the performance of LC-MS/MS in data-dependent and -independent acquisition modes and PEA Olink 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. In a next step, 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 prove their complementary strengths. We demonstrated a significant gain in proteome coverage depth and subsequent biological insight by platforms combination – a promising approach for future biomarker and mechanistic studies.

Comparison of two multiplexed technologies for profiling >1,000 serum proteins that may associate with tumor burden

“…Latest innovations in multiplex proteomics technologies have become attractive tools for mapping the circulating cancer proteome, with the hopes of giving novel insight into tumor progression and discovery of potential biomarkers to improve clinical management. 16 As the concept of personalized tumor markers were kept in mind, 6,7 we aimed to compare the feasibility of two fundamentally different targeted multiplex proteomics technologies, PEA and QKA, to measure serological proteins that may correspond to tumor burden in specific patients. To accomplish this aim, we employed the PEA and QKA technologies to simultaneously measure 1073 and 1000 proteins, respectively, in before and after surgical sera from nine OC patients (18 samples total), with two control duplicates (4 samples in total).…”

Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification

“…An expanding selection of multiplexed proteomics tools has enabled multiplatform approaches to biomarker discovery. A multiplatform investigation revealed complementarity and correlation of PEA to untargeted LC-MS/MS in the detection and quantification of plasma proteins ( 144 ). Graumann et al.…”

Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade

“…Affinity based proteomic technologies are well suited for characterizing low abundance proteins, and combining unbiased MS proteomics, with large, targeted affinity-based array technologies is a powerful, emerging strategy for the identification of biomarker candidates. The performance of LC-MS/MS and affinity-based array technologies were evaluated in a study of 173 human plasma samples [158]. LC-MS/MS was performed in the DIA and DDA modes using a Q Exactive HF instrument (Thermo) and affinity proteomics used the Olink PEA platform to measure the relative abundance of 736 protein analytes.…”