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 cross-linking, 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). Alzheimer disease (AD) 1 is the most prevalent neurodegenerative disorder worldwide. A defining pathological hallmark of AD is the deposition of plaques, largely consisting of the 40 -42-amino acid amyloid -peptide (A). A is generated by the consecutive cleavage of the amyloid precursor protein (APP) by two proteases, -secretase and ␥-secretase (1). Less than 10% of all AD cases are inherited. All mutations known to date that lead to early onset familial forms of AD occur either in APP itself or in protein components of the ␥-secretase complex (2). Although a large body of literature exists that establishes the importance of a few key proteins for AD, our understanding of the cellular context in which these proteins operate is sketchy at best. It has, for example, long been hypothesized that APP represents a transmembrane receptor. However, despite the presence of a large and structurally complex extracellular domain within this protein, to this date no extracellular APP ligand has been firmly established as a physiological interactor. The significance of a recently reported in vitro interaction between F-spondin and a recombinant APP construct consisting of a conserved central extracellular domain of APP fused to GST remains to be established (3). Early studies suggested binding of APP to the intracellular GTP-binding protein G o (4). Various other intracellular interactions of APP, in particular with proteins (FE65, mDab1, X11␣, and Shc) that bear phosphotyrosine interaction domains, have been reported (5-7). Most of these phosphotyrosine interaction domain-mediated interactions involve an NPXY motif present in the C-terminal domain of APP but are, somewhat surprisingly, observed to be independent of the phosphorylation status of the tyrosine within this motif (8). Following phosphorylation of FE65, a trimeric complex consisting of the APP intracellular domain (AICD), FE65 and the From the