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Peptides are important native molecules responsible for a wide range of biological functions within the central nervous system.\u00a0However, peptidome profiling in host brain during <jats:italic>T. gondii<\/jats:italic> infection has never been investigated. Using\u00a0a label-free peptidomics approach (LC\u2013MS\/MS), we identified a total of 2,735 endogenous peptides from acutely infected, chronically infected and control brain samples following <jats:italic>T. gondii<\/jats:italic> infection. Quantitative analysis revealed 478 and 344 significantly differentially expressed peptides (DEPs) in the acute and chronic infection stages, respectively.\u00a0Functional analysis of DEPs by Gene Ontology suggested these DEPs mainly\u00a0originated from\u00a0cell part and took part in cellular process. We also identified three novel neuropeptides derived from the precursor protein cholecystokinin. 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