Modular interaction domains that recognize peptide motifs in target proteins can impart selectivity in signaling pathways. Phosphotyrosine binding (PTB) domains are components of cytoplasmic docking proteins that bind cell surface receptors through NPXY motifs. We have employed a library of human proteome-derived NXXY sequences to explore PTB domain specificity and function. SPOTS peptide arrays were used to create a comprehensive matrix of receptor motifs that were probed with a set of 10 diverse PTB domains. This approach confirmed that individual PTB domains have selective and distinct recognition properties and provided a means to explore over 2,500 potential PTB domain-NXXY interactions. The results correlated well with previously known associations between full-length proteins and predicted novel interactions, as well as consensus binding data for specific PTB domains. Using the Ret, MuSK, and ErbB2 receptor tyrosine kinases, we show that interactions of these receptors with PTB domains predicted to bind by the NXXY arrays do occur in cells. Proteome-based peptide arrays can therefore identify networks of receptor interactions with scaffold proteins that may be physiologically relevant.External signaling molecules typically bind receptors that span the plasma membrane and thereby activate intracellular targets. This is often achieved through the selective recognition of short peptide motifs in receptors by proteins containing modular interaction domains. These binding events form the backbone of cellular signaling, and their regulation is a fundamental process by which cells organize their growth and survival (60, 62).Posttranslational modifications represent an important mechanism by which cell surface receptors recruit cytoplasmic targets (61, 67). Tyrosine phosphorylation of receptor tyrosine kinases (RTKs), cytokine receptors and adhesion proteins, for example, creates recognition motifs for the Src homology 2 (SH2) or PTB (phosphotyrosine binding) domains of cytoplasmic proteins that control responses such as cytoskeletal organization, metabolism, survival, differentiation, and division.PTB domains are found in scaffold proteins that often contain additional modular domains and motifs and thereby nucleate the formation of multiprotein complexes (24,37,50,79). They have been grouped into three broad families (insulin receptor substrate 1 [IRS-1]/Dok-like, Shc-like, and Dab-like) based on structural comparisons (75). The minimal PTB domain fold consists of a central -sandwich comprised of seven antiparallel -strands that is capped on one end by the Cterminal ␣-helix and on the other by a variable length ␣-helix found between strands 1 and 2 (or 2 and 3). Additional helices can be present in members of the Shc and Dab families. The canonical peptide-binding groove is located between the fifth -strand and the conserved C-terminal ␣-helix. Peptide ligands typically adopt a -turn that provides an anchor point for binding and is often initiated by Ϫ3 asparagine and Ϫ2 proline residues (relative to ty...