15N-labeled full-length apolipoprotein E4 as an internal standard for mass spectrometry quantification of apolipoprotein E isoforms.

Apolipoprotein E isoforms (apoE2, apoE3, and apoE4) affect the likelihood of developing Alzheimer's disease (AD), with the apoE4 isoform being a major risk factor. However, the underlying mechanism remains to be determined. ApoE isoforms vary by a single amino acid change, and it is a challenge to distinguish them on the protein level. We developed a mass spectrometry-based quantitative method utilizing (15)N-labeled full-length apoE4 ((15)N-apoE4) as an internal standard to quantify concentrations of the specific apoE4 isoform and total apoE. The measurements were performed on control and severe AD samples from human postmortem brain in a single experimental run with a single internal standard, (15)N-apoE4. By subtracting apoE4 from total apoE, the concentration of apoE2 or apoE3 for individuals possessing ε2/ε4 or ε3/ε4 alleles can be assessed. Moreover, using the full-length (15)N-apoE4 standard for the set of samples with pure ε2/ε2, ε3/ε3, or ε4/ε4 genotypes makes possible comparison of changes that occur in individual apoE2, apoE3, or apoE4 isoforms, respectively. Overall, using this method, it is possible to study the differences between apoE isoform functions on the protein level and therefore to understand the underlying biological mechanism by which apoE alters AD susceptibility.