Experimental design. (A) Brain tissues from AD patients and non-AD control subjects were analyzed to determine differential protein expression. Three groups (non-AD, APOE 3/3 (33 N), AD APOE 3/3 (33D), and AD APOE 4/4 (44D)) were compared to each other. (B) A similar analysis was performed in the CSF samples of the same patients; (C) human blood serum from AD patients (D, APOE genotype-independent) and non-AD control subjects (N) were analyzed to investigate the distribution of protein isoforms of several proteins, including ApoA-1, ApoE, ApoH, and ApoJ. (D) The distribution of differentially charged protein isoforms of ApoE was analyzed in the blood of AD patients compared with non-AD control subjects by using the recombinant human ApoE protein as reference to determine charge-isoform distribution and migration patterns. (E) Similar experiments were carried out on a group of de-identified samples with unknown disease status. (F) The pattern of isoelectric distribution of the unknown subjects was compared with the reference panel developed in E. (G) The distribution of ApoE charge-isoforms was used as reference to predict the disease states and the APOE genotypes of the unknown samples.