Abstract: Background and Objectives: The initiating steps and precise pathway of breast tumorigenesis are poorly understood and it is unclear if Ductal Carcinoma In Situ (DCIS) progresses to invasive ductal carcinoma (IDCA) of the breast. This study was undertaken to identify proteins that are differentially expressed between IDCA and DCIS and that may predict the invasive potential of breast tumors. Methodology: It is utilized that the two-dimensional difference in gel electrophoresis technology (2D-DIGE) and tandem mass spectrometry (LC-MS/MS) to perform proteomic analysis of IDCA (MCF-7 and BT-474) and DCIS (HCC-1500 and HCC-38) cell lines. Results: Identified 10 proteins that were differentially expressed between IDCA and DCIS (≥2-fold difference; p≤0.05) and classified the proteins according to their Gene Ontology (GO). Out of these proteins, 60 kDa mitochondrial heat shock protein (HSPD1), Heat Shock Protein Beta 1 (HSPB1) and the voltage-dependent anion-selective channel protein 1 (VDAC1) are over expressed in IDCA compared to DCIS. Conclusion: The functional role of the differentially expressed proteins suggests that they may serve as biomarkers for identification of tumors with invasive potential.