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The datasets presented in this article are related to the research articles entitled âNeutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsiesâ (Bennike et al., 2015 [1]), and âProteome Analysis of Rheumatoid Arthritis Gut Mucosaâ (Bennike et al., 2017 [2]). The colon mucosa represents the main interacting surface of the gut microbiota and the immune system. Studies have found an altered composition of the gut microbiota in rheumatoid arthritis patients (Zhang et al., 2015; Vaahtovuo et al., 2008; Hazenberg et al., 1992) [5â7] and inflammatory bowel disease patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) [8â10]. Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We conducted the sample preparation and liquid chromatography mass spectrometry (LC-MS/MS) analysis of all samples in one batch, enabling label-free comparison between all biopsies. The datasets are made publicly available to enable critical or extended analyses. The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples. Keywords: Colon mucosa, Proteomics, Rheumatoid arthritis, Ulcerative colitis, Inflammatory bowel diseases, Neutrophil extracellular traps, Dataset, Sigmoidoscopy, Colonoscopy |
