Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics

The dynamic range challenge for the
detection of proteins
and their
proteoforms in human plasma has been well documented. Here, we use
the nanoparticle protein corona approach to enrich low-abundance proteins
selectively and reproducibly from human plasma and use top-down proteomics
to quantify differential enrichment for the 2841 detected proteoforms
from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down
detection of proteoforms between ∼1 μg/mL and ∼10
pg/mL in absolute abundance, providing up to a 105-fold
increase in proteome depth over neat plasma in which only proteoforms
from abundant proteins (>1 μg/mL) were detected. The ability
to monitor medium and some low-abundant proteoforms through reproducible
enrichment significantly extends the applicability of proteoform research
by adding depth beyond albumin, immunoglobins, and apolipoproteins
to uncover many involved in immunity and cell signaling. As proteoforms
carry unique information content relative to peptides, this report
opens the door to deeper proteoform sequencing in clinical proteomics
of disease or aging cohorts.