Apolipoprotein E (apoE) is a 317-amino-acid long glycoprotein with three common isoforms (apoE2, apoE3, and apoE4) encoded by three apoE alleles (ε2, ε3, and ε4). These polymorphic forms arise from single amino acid substitutions with Cys and Arg interchanged at positions 112 and 158 (mature protein)1. Measuring the cerebrospinal fluid (CSF) concentrations of total apoE and the specific isoforms might provide new insights to neurological processes and neuropathogenesis. This method employs a bottom-up approach to quantify each individual apoE isoform concentration and the total concentration of apoE in CSF. Following sequential denaturation, reduction, and alkylation, the proteins are enzymatically cleaved with trypsin to liberate peptides. The resulting CSF digests are then injected into an LC-MS/MS system. Five surrogate apoE peptides are monitored. The peptides CLAVYQAGAR (abbreviated as CLAVY) and LGADMEDVR (abbreviated LGAD) were selected as specific peptide for apoE2 and E4, respectively. The peptide LGADMEDVCGR (abbreviated as LGAD-C) was selected as a common peptide for apoE2 and apoE3, while the peptide LAVYQAGAR (abbreviated as LAVY) was used as a common peptide for apoE3 and apoE4. The peptide SELEEQLTPVAEETR (abbreviated as SELEE) was selected as a common peptide of all three isoforms.