Comparing Data-Independent Acquisition and Parallel Reaction Monitoring in Their Abilities To Differentiate High-Density Lipoprotein Subclasses

High-density
lipoprotein (HDL) is a diverse group of particles
with multiple cardioprotective functions. HDL proteome follows HDL
particle complexity. Many proteins were described in HDL, but consistent
quantification of HDL protein cargo is still a challenge. To address
this issue, the aim of this work was to compare data-independent acquisition
(DIA) and parallel reaction monitoring (PRM) methodologies in their
abilities to differentiate HDL subclasses through their proteomes.
To this end, we first evaluated the analytical performances of DIA
and PRM using labeled peptides in pooled digested HDL as a biological
matrix. Next, we compared the quantification capabilities of the two
methodologies for 24 proteins found in HDL2 and HDL3 from 19 apparently healthy subjects. DIA and PRM exhibited
comparable linearity, accuracy, and precision. Moreover, both methodologies
worked equally well, differentiating HDL subclasses’ proteomes
with high precision. Our findings may help to understand HDL functional
diversity.