biostudies-literatureHan S?333 Project? of Jiangsu ProvinceNational Center for Research ResourcesWisconsin Alumni Research FoundationNIA NIH HHSNational Institute of Diabetes and Digestive and Kidney DiseasesNCRR NIH HHSNIH Office of the DirectorUniversity of Wisconsin-MadisonNational Natural Science Foundation of ChinaNational Institute of General Medical SciencesNational Institute on AgingSchool of Pharmacy, University of Wisconsin?MadisonDivision of ChemistryNIDDK NIH HHSNIGMS NIH HHSQinglan Project of Jiangsu Province of ChinaNIH HHS3870-3878https://www.ebi.ac.uk/biostudies/studies/S-EPMC11757003biostudies-literatureUnknown96(9)Gut microbiota can regulate host brain functions and influence various physiological and pathological processes through the brain-gut axis. To systematically elucidate the intervention of different gut environments on different brain regions, we implemented an integrated approach that combines 11-plex DiLeu isobaric tags with a "BRIDGE" normalization strategy to comparatively analyze the proteome of six brain regions in germ-free (GF)- and conventionally raised (ConvR)-mice. A total of 5945 proteins were identified and 5656 were quantifiable, while 1906 of them were significantly changed between GF- and ConvR-mice; 281 proteins were filtered with FC greater than 1.2 in at least one brain region, of which heatmap analysis showed clear protein profile disparities, both between brain regions Analytical chemistry11-Plex DiLeu Isobaric Labeling Enables Quantitative Assessment of Brain Region Protein Association Networks Impacted by the Gut Microbiome.PMC11757003R01DK071801R01 AG078794S10RR029531CHE-2108223S10 OD025084S10 OD02847381973450R21 AG065728R01 DK071801R01 AG052324S10OD025084S10OD028473R01AG052324R01 DK108259R21AG065728P41 GM108538DK108259S10 RR029531P41GM108538Li ZHuang JCui YFrost DCLiu RHan SRey FELi LShi Yfalse11-Plex DiLeu Isobaric Labeling Enables Quantitative Assessment of Brain Region Protein Association Networks Impacted by the Gut Microbiome.Gut microbiota can regulate host brain functions and influence various physiological and pathological processes through the brain-gut axis. To systematically elucidate the intervention of different gut environments on different brain regions, we implemented an integrated approach that combines 11-plex DiLeu isobaric tags with a "BRIDGE" normalization strategy to comparatively analyze the proteome of six brain regions in germ-free (GF)- and conventionally raised (ConvR)-mice. A total of 5945 proteins were identified and 5656 were quantifiable, while 1906 of them were significantly changed between GF- and ConvR-mice; 281 proteins were filtered with FC greater than 1.2 in at least one brain region, of which heatmap analysis showed clear protein profile disparities, both between brain regions 2024-01-01T00:00:00Z2024 Mar2026-06-02T13:14:44.395Z2025-04-04T02:09:20.99ZS-EPMC117570033837334810.1021/acs.analchem.3c05327