The complexity of mechanisms leading to the appearance and progression of cancer is a challenge being addressed by large-scale studies, such as proteomics. Simultaneous monitoring of thousands of proteins uncovers novel signaling mechanisms, thus revising our knowledge of tumorigenesis. Transforming growth factor (TGF)-beta is a secreted polypeptide that is known to inhibit tumor growth at the early stages of cancer, but promote metastasis at the later stages. Proteomics-based studies have significantly widened our knowledge of TGF-beta-dependent regulation of cell proliferation, apoptosis, DNA damage repair and transcription. This leads to better understanding of the TGF-beta role in human breast tumorigenesis, and opens the way for the development of novel anticancer treatments and drugs, with some of the drugs already entering clinics. This review discusses recent advances in proteomics studies of TGF-beta signaling and its contribution to the understanding and treatment of breast cancer.