Matrix metalloproteinases (MMPs) exert both pro-and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2 ؊/؊ mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2 Matrix metalloproteinase 2 (MMP-2) (also known as gelatinase A), like many of the 23 MMPs in humans, has long been associated with angiogenesis, tumor progression, and metastasis (20, 50). More recently the critical importance of MMP-2 in breast cancer metastasis was shown by Minn et al. (52), who found that the MMP2 gene was one of the four key genes in the genomic signature associated with the most virulent breast cancer lung metastases. In this model, the development of angiogenesis was highly dependent upon MMP-2 expression (23). With other new functions of MMPs that promote cancer cell growth, invasion, metastasis, and immune cell evasion (20, 50) a more complex role for MMPs than just degradation of extracellular matrix proteins is being revealed (12, 56).Contrary to their many carcinogenic roles, several MMPs are now being recognized as cancer antitargets due to their normal physiological roles in cell signaling and tissue homeostasis that are protective against cancer (62). MMP-3 overexpression reduces 12-dimethylbenz[a]anthracene (DMBA)-induced skin carcinogenesis (76); Mmp8 Ϫ/Ϫ mice treated with DMBA and the phorbol ester 12-myristate 13-acetate develop more skin papillomas and fibrosarcomas than wild-type mice (4), and Mmp12 Ϫ/Ϫ mice show increased lung carcinogenesis (30). The detailed study of individual MMPs is therefore necessary to understand their specific functions in different physiological and pathological processes, information that is necessary for protease drug target validation (62). Elucidation of each protease substrate repertoire or degradome is crucial to understanding the biological roles of MMPs (44). Genetic models of disease in mice are powerful, yet time-consuming (20,60,64), so high-content proteomic approaches using human cell systems offer great promise in understanding the biological functions of human proteases (60,70).