During the past decade, various genomics-based techniques have been applied with increasing success to the molecular characterisation of breast tumours, which has resulted in a more detailed classification scheme and has produced clinical diagnostic tests, which have been applied to both the prognosis and the prediction of outcome to treatment. Application of proteomics-based techniques is also seen as crucial if we are to develop a systems biology approach to the discovery of biomarkers of early diagnosis, prognosis and prediction of outcome to breast cancer therapies. However, proteomics is met with greater challenges to overcome that include optimising specimen handling and preparation, as well as determining the most appropriate proteomic platforms to apply to the identification of differentially expressed biomarker candidates and their subsequent validation. In this review, we explore some of the issues involved in specimen sampling for biomarker screening, proteomic methodologies used to identify biomarkers from clinical specimens including the isobaric tags for relative and absolute quantification (iTRAQ) system as well as strategies to validate biomarkers such as monitoring initiated detection and sequencing-multiple reaction monitoring (MIDAS-MRM). The ultimate goal is to be able to combine both genomics and proteomics-based approaches to the screening, discovery and validation of biomarkers of breast cancer that will help us move towards the individualisation and optimisation of treatment for patients.