The molecular and cellular mechanisms underlying the multistage processes of cancer progression and metastasis are complex and strictly depend on the interplay between tumor cells and surrounding tissues. Identification of protein aberrations in cancer pathophysiology requires a physiologically relevant experimental model. The mouse offers such a model to identify protein changes associated with tumor initiation and progression, metastasis development, tumor/microenvironment interplay, and treatment responses. Furthermore, the mouse model offers the ability to collect samples at any stage in tumor development from highly matched disease cases and controls with identical environmental and genetic backgrounds, thus providing an excellent method for biomarker discovery. Xenograft and genetically engineered mouse models have been widely used to identify proteomic patterns in tumor tissues and plasma samples associated with different stages of human cancer, including early cancer detection and development of metastasis. Here, we review proteomic strategies to identify proteins involved in key cancer processes within such animal models as well as biomarkers for diagnosis, prognosis, and monitoring of cancer progression and treatment response. Central to such studies is the ability to ensure at an early stage that the identified proteins are of clinical relevance by examining relevant specimens from larger cohorts of cancer patients.