Monitoring protein biomarkers in cerebrospinal fluid (CSF) of patients with Alzheimer’s Disease (AD) has been highly beneficial to understanding disease progression. While several CSF biomarkers can reproducibly distinguish normal and diseased samples, CSF is a difficult biological fluid to obtain in research studies. The need for blood-based biomarkers of AD has driven a continuous search for novel candidates. Here we report the development of a multiplex immunoassay to quantitatively measure seven proteins present in both CSF and blood that are involved in neurological disease: Neurogranin, TREM2, ApoE4, FABP3, Ferritin, angiogenin, and prion protein. Notably, presence of the APOE4 allele is prominently associated with an increased risk for AD, in comparison to the APOE2 and APOE3 alleles. Although these ApoE isoforms differ at only one or two amino acids, our assay distinguished ApoE4 with minimal cross-reactivity. Using this novel immunoassay, we measured these 7 biomarkers in CSF, plasma, and serum from AD patients and healthy controls. Additionally, we developed an ultrasensitive Single Molecule Counting (SMC) assay for amyloid beta 1-42 (Aβ42). This kit could detect the Aβ42 peptide in CSF and plasma at sub-pg/mL concentrations. This study demonstrates the value of evaluating both novel and established biomarkers of neurodegeneration across distinct sample types.