Using a targeted peptide-centric proteomics approach, we performed in vitro protease substrate profiling of the apoptotic serine protease granzyme B resulting in the delineation of more than 800 cleavage sites in 322 human and 282 mouse substrates, encompassing the known substrates Bid, caspase-7, lupus La protein, and fibrillarin. Triple SILAC (stable isotope labeling by amino acids in cell culture) further permitted intra-experimental evaluation of species-specific variations in substrate selection by the mouse or human granzyme B ortholog. For the first time granzyme B substrate specificities were directly mapped on a proteomic scale and revealed unknown cleavage specificities, uncharacterized extended specificity profiles, and macromolecular determinants in substrate selection that were confirmed by molecular modeling. We further tackled a substrate hunt in an in vivo setup of natural killer cell-mediated cell death confirming in vitro Because macromolecular properties present in protease substrates guide cleavage recognition, specificity, and efficiency beyond canonical cleavage sites, the necessity to determine protease substrates directly in a natural proteome and even in a species-specific context strikingly became important to fully elucidate proteolytic actions. Together with recent advances in the development of protease-targeted activity-based probes, systematic high throughput methods with broad applicability for the identification of (individual) in vitro and in vivo protease substrate repertoires have recently emerged (1).Granzyme B (GrB), 1 a serine protease that recognizes aspartic acid in the substrate P1 position, is contained within the secretory granules of cytotoxic T lymphocytes and natural killer (NK) cells (2) and gains entry into transformed or virally infected target cells by the pore-forming protein perforin (3). Once delivered in targets cells, GrB can promote apoptosis either by activation of the caspase cascade (4) or by directly cleaving substrate proteins (5-10). Next to a few reported extracellular (11) and viral substrates (12) only about 60 possible cellular mammalian GrB substrates have been identified to date mainly by non-systematic approaches. Only for a few of these, physiological relevance was shown and occasionally in a species-specific context (13-15) as it was only recently found that human and mouse granzyme B signal via overlapping as well as distinct apoptotic pathways.The substrate specificity of mouse, human, and rat GrB was profiled previously by positional scanning combinatorial libraries of short tetrapeptides from P4 to P1 and, using phage display, for mouse and human GrB somewhat extended to P2Ј (13,(15)(16)(17). By further showing that Bid is a very poor substrate for mGrB, in sharp contrast to its very efficient cleavage by hGrB, contradictory results obtained by using recombinant GrB from different species were elucidated (13-15). Next to GrB, GrA was also reported to display altered substrate specificity and functionality fueled by structural differences...