Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

The Proteograph Product Suite, a multiplexed nanoparticle
(NP)
protein corona-based workflow, substantially improves the depth of
detection of proteins by mass spectrometry (MS) by compressing the
dynamic range of protein abundances. Here, we evaluate its quantitative
performance and suitability for large-scale studies. Using multispecies
spike-in experiments, we assessed fold change accuracy, linearity,
precision, and the lower limit of quantification (LLOQ) across multiple
MS platforms. Combined with the Orbitrap Astral MS, the Proteograph
XT assay enabled identification of more than 7,000 plasma proteins.
In mixed-species dilution experiments, fold change accuracy was preserved,
with Proteograph quantifying 3.5 times more proteins than the Neat
plasma workflow at the same fold change error threshold. Similar accuracy
was observed with the Orbitrap Exploris 480 MS, and we also demonstrate
that different proteome backgrounds do not impact the accuracy. Data
produced with NPs from the four distinct NP batches (each supporting
>100,000 assays) showed only a 4% increase in protein intensity
CV
across batches. Together, these results demonstrate that the Proteograph
Product Suite provides depth as well as quantitative accuracy and
precision to power new biomarker discovery and biological understanding
in population-scale plasma proteomics cohorts.