biostudies-literatureMa MNIDDK NIH HHSNIA NIH HHSU.S. Department of Health & Human Services | NIH | National Institute on AgingU.S. Department of Health & Human Services | NIH | National Cancer InstituteNHLBI NIH HHSU.S. Department of DefenseU.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood InstituteNCI NIH HHSU.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases7736https://www.ebi.ac.uk/biostudies/studies/S-EPMC9751300biostudies-literatureUnknown13(1)Accurate, in-depth mapping of proteins on whole-tissue levels provides comprehensive insights into the spatially-organized regulatory processes/networks in tissues, but is challenging. Here we describe a micro-scaffold assisted spatial proteomics (MASP) strategy, based on spatially-resolved micro-compartmentalization of tissue using a 3D-printed micro-scaffold, capable of mapping thousands of proteins across a whole-tissue slice with excellent quantitative accuracy/precision. The pipeline includes robust tissue micro-compartmentalization with precisely-preserved spatial information, reproducible procurement and preparation of the micro-specimens, followed by sensitive LC-MS analysis and map generation by a MAsP app. The mapping accuracy was validated by comparing the MASP-generated maps ofNature communicationsIn-depth mapping of protein localizations in whole tissue by micro-scaffold assisted spatial proteomics (MASP).PMC9751300CA224434W81XWH1910805R01 AG068168AG068168R01 CA224434DK124020HL103411R01 HL103411U01 DK124020An BRasam SMa MQian SXue CHuo SQu JPu JZhang MZhu XShen SWang JfalseIn-depth mapping of protein localizations in whole tissue by micro-scaffold assisted spatial proteomics (MASP).Accurate, in-depth mapping of proteins on whole-tissue levels provides comprehensive insights into the spatially-organized regulatory processes/networks in tissues, but is challenging. Here we describe a micro-scaffold assisted spatial proteomics (MASP) strategy, based on spatially-resolved micro-compartmentalization of tissue using a 3D-printed micro-scaffold, capable of mapping thousands of proteins across a whole-tissue slice with excellent quantitative accuracy/precision. The pipeline includes robust tissue micro-compartmentalization with precisely-preserved spatial information, reproducible procurement and preparation of the micro-specimens, followed by sensitive LC-MS analysis and map generation by a MAsP app. The mapping accuracy was validated by comparing the MASP-generated maps of2022-01-01T00:00:00Z2022 Dec2026-05-29T04:28:53.686Z2024-11-13T23:25:48.755ZS-EPMC97513003651748410.1038/s41467-022-35367-2