Brain metastases are a devastating consequence of cancer and currently there are no specific biomarkers or therapeutic targets for risk prediction, diagnosis, and treatment. Here the proteome of the brain metastatic breast cancer cell line 231-BR has been compared with that of the parental cell line MDA-MB-231, which is also metastatic but has no organ selectivity. Using SILAC and nanoLC-MS/MS, 1957 proteins were identified in reciprocal labeling experiments and 1584 were quantified in the two cell lines. A total of 152 proteins were confidently determined to be up-or down-regulated by more than twofold in 231-BR. Of note, 112/152 proteins were decreased as compared with only 40/152 that were increased, suggesting that down-regulation of specific proteins is an important part of the mechanism underlying the ability of breast cancer cells to metastasize to the brain. When matched against transcriptomic data, 43% of individual protein changes were associated with corresponding changes in mRNA, indicating that the transcript level is a limited predictor of protein level. In addition, differential miRNA analyses showed that most miRNA changes in 231-BR were up-(36/45) as compared with down-regulations (9/45). Pathway analysis revealed that proteome changes were mostly related to cell signaling and cell cycle, metabolism and extracellular matrix remodeling. The major protein changes in 231-BR were confirmed by parallel reaction monitoring mass spectrometry and consisted in increases (by more than fivefold) in the matrix metalloproteinase-1, ephrin-B1, stomatin, myc target-1, and decreases (by more than 10-fold) in transglutaminase-2, the S100 calcium-binding protein A4, and L-plastin. The clinicopathological significance of these major proteomic changes to predict the occurrence of brain metastases, and their potential value as therapeutic targets, warrants further investigation. Brain metastases affect 10 -20% of cancer patients with disseminated disease (1). Even small lesions can cause neurological disability, and the median survival time of patients with brain metastases is short, with about 80% mortality within one year of diagnosis. The molecular basis of cancer metastases to the brain remains unknown and with advances in the control of systemic disease, the incidence of brain metastases is increasing (1, 2). In the case of breast cancer, brain relapse typically occurs years after primary tumor excision, suggesting that disseminated breast cancer cells must first acquire specialized functions to invade and grow in this organ (3). Retrospective studies of breast cancer patients with brain metastases found that a young age at diagnosis, primary tumors that are estrogen receptor negative or overexpressing the human epidermal growth factor receptor 2 (HER2) 1 and/or epidermal growth factor receptor, and the From the ‡School