Dysregulated protease activity is often implicated in the initiation of inflammation and immune cell recruitment in gastrointestinal inflammatory diseases. Using N-terminomics/TAILS (terminal amine isotopic labeling of substrates), we compared proteases, along with their substrates and inhibitors, between colonic mucosal biopsies of healthy patients and those with ulcerative colitis (UC). Among the 1642 N-termini enriched using TAILS, increased endogenous processing of proteins was identified in UC compared to healthy patients. Changes in the reactome pathways for proteins associated with metabolism, adherens junction proteins (E-cadherin, liver-intestinal cadherin, catenin alpha-1, and catenin delta-1), and neutrophil degranulation were identified between the two groups. Increased neutrophil infiltration and distinct proteases observed in ulcerative colitis may result in extensive break down, altered processing, or increased remodeling of adherens junctions and other cellular functions. Analysis of the preferred proteolytic cleavage sites indicated that the majority of proteolytic activity and processing comes from host proteases, but that key microbial proteases may also play a role in maintaining homeostasis. Thus, the identification of distinct proteases and processing of their substrates improves the understanding of dysregulated proteolysis in normal intestinal physiology and ulcerative colitis.P roteases are implicated in key functions during gastrointestinal (GI) homeostasis, and dysregulated proteolysis is one of the contributing factors of gastrointestinal inflammatory diseases. 1−3 Upon recruitment to the site of inflammation, activated immune cells produce various intraand extra-cellular proteases including neutrophil elastase (NE), matriptase, cathepsins, caspases, and matrix metalloproteinases, which all play roles in modulating the host response. 4−7 The shift in the balance between regulated and dysregulated proteolysis in GI inflammation is not fully understood, and the full repertoire of proteases, their substrates, and their inhibitors has not been examined in detail. Transcript analyses have been performed on samples from patients with inflammatory bowel diseases, 8 but mRNA levels often do not correlate with protein levels. 9 Furthermore, transcriptomics does not assess whether a substrate is cleaved or not by a