The proteins coimmunoprecipitated with apoE4 in the membrane extracts from mouse brain. Mouse brain membrane extracts were applied to the FLAG-apoE4(1–299) or FLAG-apoE4(1–272)-anti-FLAG M2-agarose affinity resin column and then eluted with the elution buffer. The eluant was dialyzed against the dialysis buffer, concentrated, and subjected to SDS-PAGE. The gels were stained with SilverQuest Silver Staining kit (Invitrogen). The protein bands (arrows), which were absent in the brain samples without apoE4s, and in the apoE4s samples without brain, were subjected to LC-MS/MS analysis.