ABSTRACT The mammalian secretory pathway regulates a cell’s extracellular interactions by making most signals and receptors that moderate communication. Furthermore, it makes cell adhesion molecules and the extracellular matrix components. Indeed it makes most proteins needed for a cell to interact with its extracellular environment, which includes ~⅓ of their protein-coding genes in the human genome. The pathway has hundreds of machinery proteins used for synthesizing and trafficking secreted proteins, but each of these have their unique role in the process. However, for the ~8000 protein products of the secretory pathway, it remains unclear what machinery is needed for each one. To further complicate this, each tissue expresses its own subset of genes for the secretory pathway. Understanding the organization of the pathway and the interactions between the secretory pathway machinery and secreted protein products is of considerable importance since many diseases involve changes in the abundance of secreted and/or membrane proteins, and these are not always accompanied by changes in mRNA. That is, the secretory pathway itself is regulating changes in hormone secretion, managing ER stress, or amyloid formation. Thus, there is a fundamental need to understand (1) what the secretory pathway machinery does, (2) which secreted and membrane proteins rely upon it, (3) how the hundreds of machinery proteins work together, and (4) what regulates their functions. All of these items require systems-level experiments, tools, and analyses to fully understand. Here we are developing such resources for the community to answer fundamental questions. In this work, we are mapping out all of the secretory pathway machinery and detailing their functions. We describe their functions mathematically, and build computational models to account for their concerted functions, even for individual tissues and cell types. Furthermore we are developing software and algorithms to help analyze the models and use them to diagnose the molecular bases underlying secretory disorders. We are further developing and deploying experimental techniques to more fully identify all of the secretory machinery proteins needed to facilitate the production of each specific secreted or membrane protein, and will use those techniques to identify these interactions for liver-secreted proteins. Finally, we are using genomics and systems biology techniques to unravel the regulatory mechanisms controlling the tissue-specific expression of the secretory pathway. Through this, valuable resources will be developed and shared with the community to make it easier to study the secretory pathway as a biomolecular system.