A human fecal metaproteomic dataset from celiac disease patients on gluten-free diet with or without poly-autoimmunity

This dataset provides the fecal metaproteome profiles of 28 celiac disease patients on a gluten-free diet, distinguished by the presence or absence of co-occurring autoimmune conditions. The resource includes raw liquid chromatography-tandem mass spectrometry (LC-MS/MS) files, database search results, protein/peptide identification outputs, and taxonomic/functional annotation outputs, along with comprehensive anthropometric, clinical, and dietary metadata for each patient. The identified proteins originate from microbial, human, and plant sources, consistent with the multi-database search strategy used. This collection is designed for reuse in meta-analyses and integrative studies exploring functional changes in the gut microbiome related to auto-immune status and dietary variables. The complete dataset is available via the ProteomeXchange Consortium with the identifier PXD069517.