Interorgan communication is vital for coordinating organ functions and enabling organisms to adapt to their environment. Disruptions in these networks are associated with various diseases. Despite the critical role of the secreted proteome in interorgan signaling, it remains poorly characterized due to the challenges in identifying the secreted proteins involved, which may be low in abundance and difficult to trace back to their source. The recently developed R26 BirA*G3-ER knock-in mice, featuring an engineered biotin ligase, enable the labeling of all secreted proteins within the endoplasmic reticulum of specific organs. This permits the identification of (low-abundance) secreted proteins and determination of their origins and destinations. Here, we present a detailed protocol for using conditional R26 BirA*G3-ER knock-in mice, followed by the enrichment and identification of secreted proteins trafficked to distal organs. By shedding light on secretory protein networks, this approach offers new insights into the mechanisms underlying development, homeostasis, and disease.