The field of proteomics is in its infancy; however the discipline, its technology, and our abilities to translate the proteomic data are rapidly evolving. In the near future proteomics should significantly improve our ability to make early cancer diagnoses, direct appropriate personalised therapy, and monitor response to therapy, including thermal therapy. The potential role of proteomics in breast cancer early diagnosis, prediction of aggressiveness is clear. Its potential importance in guiding treatment choice and prediction of treatment response is especially intriguing. This paper reviews the varied methodologies used in the field of proteomics, including gel-free, label-free proteomics, quantitative proteomics, phosphoproteomics, protein extraction from formalin-fixed, paraffin-embedded tissue sections (FFPE) proteomics, laser capture microdissection proteomics, and targeted proteomics. It also discusses two new areas, morphoproteomics and salivary proteomics cancer diagnostics, as well as selected pre-clinical and clinical analyses using the described methodologies. Morphoproteomics defines which signal transduction pathways exist within the tumour cells and the surrounding tissue comprising a patient's cancer biopsy specimen. Morphoproteomics, and the other histology-based proteomic techniques are actually beginning to clinically make possible individualised treatment of breast cancer. Salivary proteomics, in part because it is non-invasive, is a new area of breast cancer diagnostics that can be used to non-invasively monitor an individual patient's response to treatment with every treatment cycle. The current literature demonstrates that a diagnosis of breast cancer can be readily made using proteomic methodologies, and that proteomics can also define cancers with a poor prognosis at the time of diagnosis. With such early prognostic information we expect proteomics will soon be a science that on the basis of prognosis, guides individualised therapy and as well, have the ability to monitor the results of thermal therapy, radiation, and chemotherapy treatment during therapy.