Systematic characterization of intercellular signaling approximating the physiological conditions of stimulation that involve direct cell-cell contact is challenging. We describe a proteomic strategy to analyze physiological signaling mediated by the T-cell costimulatory receptor CD28. We identified signaling pathways activated by CD28 during direct cell-cell contact by global analysis of protein phosphorylation. To define immediate CD28 targets, we used phosphorylated forms of the CD28 cytoplasmic region to obtain the CD28 interactome. The interaction profiles of selected CD28-interacting proteins were further characterized in vivo for amplifying the CD28 interactome. The combination of the global phosphorylation and interactome analyses revealed broad regulation of CD28 and its interactome by phosphorylation. Among the cellular phosphoproteins influenced by CD28 signaling, CapZ-interacting protein (CapZIP), a regulator of the actin cytoskeleton, was implicated by functional studies. The combinatorial approach applied herein is widely applicable for characterizing signaling networks associated with membrane receptors with short cytoplasmic tails.uring some forms of intercellular communication, soluble growth factors are secreted by one cell type and bind specific transmembrane receptor tyrosine kinases (RTKs) present on neighboring cells. Activated RTKs then undergo autophosphorylation and also phosphorylate associated scaffold proteins, thereby creating docking sites for effector proteins with phosphotyrosine (pTyr)-recognition modules such as Src homology 2 (SH2) and pTyr-binding (PTB) domains (1). These immediate targets of growth-factor receptors control a variety of intracellular responses, typified by the activation of serine/ threonine protein kinases such as those involved in the ERK MAP kinase pathway. Growth-factor signaling therefore leads to extensive changes in both tyrosine and serine/threonine phosphorylation (2).The alterations in protein-protein interactions and posttranslational modifications elicited by transmembrane receptors can in principle be characterized by mass spectrometry (MS)-based proteomics (3-6). However, under circumstances that involve complex cell-cell interactions, identifying physiologically relevant signals using MS-based proteomics can be challenging. For example, obtaining a sufficiently robust response for MS analysis has often required the use of cells that overexpress a receptor of interest and are subjected to a nonphysiological stimulus. For this reason, experiments have often focused on specific, often stereotypic, aspects of the cellular response, rather than taking a more global approach. Moreover, cell-cell interactions are often typified by the interaction of multiple transmembrane receptor-ligand pairs, frequently involving membrane proteins that are not receptor kinases. Short-peptide motifs from such receptors that serve as potential ligands for downstream targets can be used as affinity probes for binding partners, but these experiments suffer from high fals...