A Technical Evaluation of Plasma Proteomics Technologies

Abstract

Plasma proteomic technologies are rapidly evolving and of critical importance to the field of biomedical research. Here we report a technical evaluation of six notable plasma proteomic technologies - unenriched (Neat), Acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph XT, Olink Explore HT. The methods were compared on proteomic depth, reproducibility, linearity, tolerance to lipid interference, and limit of detection/quantification. In total we performed 618 LC-MS/MS experiments and 93 Olink Explore HT assays. The Seer method achieved the greatest proteomic depth ([~]4,500), while Olink detected [~]2,600 proteins. Other MS-based methods ranged from [~]500-2,200. Neat, Mag-Net, Seer, and Olink had strong reproducibility, while PreOmics and Acid showed higher variability. All MS methods showed good linearity with spiked-in C-Reactive Protein (CRP); CRP was surprisingly not in the Olink assay. None of the methods were affected by lipid interference. Seer had more than double the number of quantifiable proteins (4,800) for both LOD and LOQ than the next best method. Olink was comparable to Neat and Mag-Net for LOD, but worse for LOQ. Finally, we tested the applicability of these methods for detecting differences between healthy and cancer groups in a non-small cell lung cancer (NSCLC) cohort.