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

Abstract

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.

Enrichment of apolipoprotein A-IV and apolipoprotein D in the HDL proteome is associated with HDL functions in diabetic kidney disease without dialysis

“…Digested HDL proteins (50 ng protein) were quantified by parallel reaction monitoring (PRM), as previously described [14]. Briefly, an Easy-nLC 1200 UHPLC (Thermo Scientific, Bremen, Germany) was used for peptide separation.…”

“…PRM methodology was assembled using data derived from shotgun proteomics analyses as previously described [14]. Ninety-one proteins were identified, but this number was reduced to 47 proteins after eliminating proteins that could be potential contaminants or were in low abundance (keratin, proteins with < 2 unique peptides and peptides with high interfering signal).…”

Sensitive and reproducible determination of clinical HDL proteotypes

“…We then compared our HDL proteome spectral library to previously published datasets on HDL proteome constituents including the Davidson HDL watchlist (http://homepages.uc.edu/~davidswm/HDLproteome.html, last updated August 2015) and 20 HDL proteome analysis studies published between 2015 and February 2020 that included protein annotation data (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)25). In most of these studies HDL was isolated using an ultracentrifugation protocol similar to our HDL isolation strategy.…”

HDL-proteome enrichment with apolipoprotein A-IV compensates for HDL loss of function in diabetes mellitus kidney disease

“…Selection of HDL peptides for targeted quanti cation PRM methodology was assembled from shotgun proteomics analyses as previously described [12] . Ninety-one proteins were identi ed, but this number was reduced to 47 proteins eliminating potentials contaminant proteins (keratin, proteins with <2 unique peptides and peptides with high interfering signal and mass error >10 ppm).…”