Matrix metalloproteinase-9 (MMP-9) is implicated in tumor metastasis as well as a variety of inflammatory and pathological processes. Although many substrates for MMP-9, including components of the extracellular matrix, soluble mediators such as chemokines, and cell surface molecules have been identified, we undertook a more comprehensive proteomics-based approach to identify new substrates to further understand how MMP-9 might contribute to tumor metastasis. Previous proteomics approaches to identify protease substrates have depended upon differential labeling of each sample. Instead we used a label-free quantitative proteomics approach based on ultraperformance LC-ESI-high/low collision energy MS. Conditioned medium from a human metastatic prostate cancer cell line, PC-3ML, in which MMP-9 had been downregulated by RNA interference was compared with that from the parental cells. From more than 200 proteins identified, 69 showed significant alteration in levels after depletion of the protease (>؎2-fold), suggesting that they might be candidate substrates. Levels of six of these (amyloid- precursor protein, collagen VI, leukemia inhibitory factor, neuropilin-1, prostate cancer cell-derived growth factor (PCDGF), and protease nexin-1 (PN-1)) were tested in the conditioned media by immunoblotting. There was a strong correlation between results by ultraperformance LC-ESI-high/low collision energy MS and by immunoblotting giving credence to the label-free approach. Matrix metalloproteinase-9 (MMP-9) 1 or gelatinase B was originally identified as a secreted enzyme that could degrade collagens, especially collagen IV (1, 2). These early observations have since been refined as it became apparent that denatured collagen I, IV as well as gelatin are efficiently cleaved but that intact collagen I or IV are poor substrates for the enzyme (3, 4). Indeed MMP-9 fails to promote cellular invasion of natural basement membranes (5). Although MMP-9 may not be a determining factor for invasion of collagen IV-rich basement membranes, collagen IV degradation by MMP-9 has been shown to be involved in angiogenesis. For instance, the reduced levels of antiangiogenic peptides derived from collagen IV in mice genetically deficient in MMP-9 reflect the decreased turnover of collagen IV in the absence of MMP-9 (6). Many non-collagenous substrates have also been identified as MMP-9 substrates including cell surface molecules and secreted proteins. These include molecules involved in cell adhesion, cell surface receptors, cytokines, protease inhibitors, angiogenic factors, and growth factors. The cleavage of many of these substrates affects the cellular phenotype and is associated with several pathological conditions in mice (7,8).In cancers MMP-9 produced by the host contributes to squamous cancer progression by activation of the angiogenic 1 The abbreviations used are: MMP, matrix metalloproteinase; PN-1, protease nexin-1; TIMP, tissue inhibitor of metalloproteinases; UPLC, ultraperformance LC; MS E , high/low collision energy MS; MudPIT, ...