Immunoprecipitation of APOE-lipoprotein particles with anti-pan-APOE antibodies coupled to Dynabeads for mass spectrometric phospholipidomic and proteomic analyses

We describe an immunoprecipitation protocol for the purification of APOE lipoprotein particles from human cerebrospinal fluid (CSF) suitable for subsequent phospholipidomic and proteomic analyses by mass spectrometry. The method describes the immunoprecipitation of eight CSF samples in parallel. The procedure takes two days to complete and involves an overnight coupling reaction. It is possible to carry out several immunoprecipitations of eight CSF samples during the two-day period. The protocol uses 0.4 ml of CSF, 0.025 mg of anti-pan-APOE IgG and 5 mg of Dynabeads per immunoprecipitation, and yields sufficient material for both phospholipidomic and proteomic analyses by mass spectrometry. The protocol typically produces a 15-fold enrichment of APOE relative to albumin (the most abundant CSF protein) and provides reproducible analytical results.