Background ApoAI (apolipoproteins AI) and apoAII (apolipoprotein AII) are 
structural and functional proteins of high-density lipoproteins (HDL) which 
undergo post-translational modifications at specific residues, creating distinct 
proteoforms. While specific post-translational modifications have been reported 
to alter apolipoprotein function, the full spectrum of apoAI and apoAII 
proteoforms and their associations with cardiometabolic phenotype remains 
unknown. Herein, we comprehensively characterize apoAI and apoAII proteoforms 
detectable in serum and their post-translational modifications and quantify 
their associations with cardiometabolic health indices. Methods and Results 
Using top-down proteomics (mass-spectrometric analysis of intact proteins), we 
analyzed paired serum samples from 150 CARDIA (Coronary Artery Risk Development 
in Young Adults) study participants from year 20 and 25 exams. Measuring 15 
apoAI and 9 apoAII proteoforms, 6 of which carried novel post-translational 
modifications, we quantified associations between percent proteoform abundance 
and key cardiometabolic indices. Canonical (unmodified) apoAI had inverse 
associations with HDL cholesterol and HDL-cholesterol efflux, and positive 
associations with obesity indices (body mass index, waist circumference), and 
triglycerides, whereas glycated apoAI showed positive associations with serum 
glucose and diabetes mellitus. Fatty-acid‒modified ApoAI proteoforms had 
positive associations with HDL cholesterol and efflux, and inverse associations 
with obesity indices and triglycerides. Truncated and dimerized proteoforms of 
apoAII were associated with HDL cholesterol (positively) and obesity indices 
(inversely). Several proteoforms had no significant associations with phenotype. 
Conclusions Associations between apoAI and AII and cardiometabolic indices are 
proteoform-specific. These results provide "proof-of-concept" that precise 
chemical characterization of human apolipoproteins will yield improved insights 
into the complex pathways through which proteins signify and mediate health and 
disease.