Despite intense research efforts, the physiological function and molecular environment of the amyloid precursor protein has remained enigmatic. Here we describe the application of time-controlled transcardiac perfusion crosslinking (tcTPC), a method for the in vivo mapping of protein interactions in intact tissue, to study the interactome of the amyloid precursor protein (APP). To gain insights into the specificity of reported protein interactions the study was extended to the mammalian amyloid precursor like proteins (APLP1 and APLP2). To rule out sampling bias as an explanation for differences in the individual data sets, a small-scale quantitative iTRAQ-based comparison of APP, APLP1 and APLP2 interactomes was carried out. An interactome map was derived which confirmed 8 previously reported interactions of APP and revealed the identity of more than 30 additional proteins which reside in spatial proximity to APP in the brain. Subsequent validation studies confirmed a physiological interaction between APP and leucine rich repeat and Ig domain containing protein 1 (LINGO-1), demonstrated a strong influence of LINGO-1 on the proteolytic processing of APP, and consolidated similarities in the biology of APP and p75.