Technical Evaluation of Plasma Proteomics Technologies

Plasma proteomics
technologies are rapidly evolving and of critical
importance to the field of biomedical research. Here, we report a
technical evaluation of six notable plasma proteomics technologiesunenriched
(Neat), acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph
XT, and 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 (∼4500 proteins detected), while Olink detected
∼2600 proteins. Other MS-based methods ranged from ∼500–2200
proteins detected. In our analysis, Neat, Mag-Net, Seer, and Olink
had good reproducibility, while PreOmics and Acid had higher variability
(>20% median coefficient of variation). 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 produced the highest number of quantifiable proteins
with a measurable LOD (4407) and LOQ (2696). Olink had the next highest
number of quantifiable proteins, with 2002 having an LOD and 1883
having an LOQ. Finally, we tested the applicability of these methods
for detecting differences between healthy and cancer groups in a nonsmall
cell lung cancer (NSCLC) cohort. All six methods detected differentially
abundant proteins between the cancer and healthy samples but disagreed
on which proteins were significant, highlighting the contrast between
each method.