Breast cancer is the second leading cause of cancer death for women in the 
United States. Of the different subtypes, estrogen receptor-negative (ER(-)) 
tumors, which are ErbB2+ or triple-negative, carry a relatively poor prognosis. 
In this study, we used system-wide analysis of breast cancer proteomes to 
identify proteins that are associated with the progression of ER(-) tumors. Our 
two-step approach included an initial deep analysis of cultured cells that were 
obtained from tumors of defined breast cancer stages, followed by a validation 
set using human breast tumors. Using high-resolution mass spectrometry and 
quantification by Stable Isotope Labeling with Amino Acids in Cell Culture 
(SILAC), we identified 8,750 proteins and quantified 7,800 of them. A 
stage-specific signature was extracted and validated by mass spectrometry and 
immunohistochemistry on tissue microarrays. Overall, the proteomics signature 
reflected both a global loss of tissue architecture and a number of metabolic 
changes in the transformed cells. Proteomic analysis also identified high levels 
of IDH2 and CRABP2 and low levels of SEC14L2 to be prognostic markers for 
overall breast cancer survival. Together, our findings suggest that global 
proteomic analysis provides information about the protein changes specific to 
ER(-) breast tumor progression as well as important prognostic information.