Discovery of better biomarkers for diagnosis, prognosis and therapy-response prediction is the most critical task of a scientific quest aimed at developing novel, tailormade therapies for patients with cancer. Consequently, a proteome-wide analysis, in addition to genomic studies, is an absolute requirement for a complete functional understanding of tumor biology. Ultra-sensitive, high-performance Fourier-transform ion-cyclotron resonance (FTICR) mass spectrometry (MS) currently holds an important role in fulfilling the demands of biomarker discovery. In this review, we describe the applicability of FTICR-MS for breast cancer proteomics, particularly for the analysis of complex protein mixtures obtained from a limited number of cells typically available from clinical specimens.