The brain reveals a complex architecture of > 150 distinct regions. Over the last decade tremendous efforts have been undertaken to elucidate the molecular organization of these subregions. Various consortia mapped the human brain morphology, structure, and function using imaging and RNA expression profiling. This study adds to these approaches by providing a comprehensive, quantitative protein expression map of 13 anatomically distinct brain regions covering over 11,000 proteins (Tueshaus et al., 2023)Recent technical progress in the area of liquid chromatography, mass spectrometry and data analysis, advanced the sensitivity and reproducibility of LC-MS measurements. However, a high-throughput tissue diagnostics setup remains elusive. Therefore, we coupled a micro-flow LC (fast, robust) to a timsTOF-HT (fast, sensitive) in order to establish a system that can deliver speed while maintaining deep proteome coverage. Optimizing the proteomic workflow involved brain tissue-specific sample preparation, including delipidation. With this efficient workflow, we analyzed three biological replicates of thirteen postmortem human brain regions, identifying over 9,500 protein groups in each. Bioinformatic analysis revealed distinctive profiles among brain regions, showcasing regional driver protein candidates. While a shared core proteome existed, unique fingerprints pointed to specific functions and cellular compositions. To facilitate data exploration, a purpose-built R Shiny app (https://brain-region-atlas.proteomics.ls.tum.de) is provided for the scientific community.This project not only introduced the efficacy of combining micro-flow LC with timsTOF-HT as a fast, robust, and sensitive LC-MS setup but also deepened our understanding of the proteomic profiles across thirteen human brain regions.