The astacin-like zinc-dependent metalloendopeptidase human meprin (hmeprin) (EC 3.4.24.18) was first discovered in 1982 for its ability to hydrolyze N-benzoyl-l-tyrosyl-p-aminobenzoic acid, a chymotrypsin substrate used for assessing exocrine pancreas function [1]. N-benzoyl-l-tyrosyl-p-aminobenzoic acid hydrolase (PPH) was subsequently purified and characterized from human small intestinal mucosa [2]. At the same time, PPH orthologs, called meprin (metal endopeptidase from renal tissue) or endopeptidase-2, were found in mouse and rat kidney, respectively [3,4]. Two similar subunits, termed meprina and meprinb, with molecular masses of 95 and 105 kDa, respectively, were identified. Human meprin cDNA was expressed in Madin-Darby canine kidney (MDCK) cells, a wellestablished cell system for polarized epithelial cells. To date, no such thoroughly characterized model system exists for human epithelial cells. Hmeprina is secreted into the culture medium of MDCK cells as inactive homodimers, whereas hmeprinb is primarily membrane-bound [5]. Hence, heterodimers of hmeprina ⁄ b allowed for localization of the a-subunit to the plasma membrane [6]. Inactive zymogens of hmeprina and b are processed by limited proteolysis with trypsin into their active forms [5,6]. Hmeprina, but not b, may alternatively be activated by plasmin [7,8].A first step towards the elucidation of the biological function of meprin was achieved by testing putatively cleavable polypeptide substrates. A variety of protein and peptide substrates were processed in vitro; In the past, protease-substrate finding proved to be rather haphazard and was executed by in vitro cleavage assays using singly selected targets. In the present study, we report the first protease proteomic approach applied to meprin, an astacin-like metalloendopeptidase, to determine physiological substrates in a cell-based system of Madin-Darby canine kidney epithelial cells. A simple 2D IEF ⁄ SDS ⁄ PAGE-based image analysis procedure was designed to find candidate substrates in conditioned media of MadinDarby canine kidney cells expressing meprin in zymogen or in active form. The method enabled the discovery of hitherto unkown meprin substrates with shortened (non-trypsin-generated) N-and C-terminally truncated cleavage products in peptide fragments upon LC-MS ⁄ MS analysis. Of 22 (17 nonredundant) candidate substrates identified, the proteolytic processing of vinculin, lysyl oxidase, collagen type V and annexin A1 was analysed by means of immunoblotting validation experiments. The classification of substrates into functional groups may propose new functions for meprins in the regulation of cell homeostasis and the extracellular environment, and in innate immunity, respectively.Abbreviations ADAM, a disintegrin and metalloprotease; BMP-1, bone morphogenetic protein 1; CID, collision-induced dissociation; ECM, extracellular matrix; hmeprin, human meprin (EC 3.4.24.18); ICAT, isotope-coded affinity tag; MDCK, Madin-Darby canine kidney; MMP, matrix metalloproteinase; PPH, N-benzoyl-L-tyr...