Adult neurogenesis is restricted to a few niches in the adult mammalian brain. Despite the importance of the local environment in these niches, there is no comprehensive characterization of the niche-specific extracellular matrix (ECM) and associated proteins available. Using state-of-the-art mass spectrometry workflows we present a comprehensive proteomic characterization of the subventricular zone (SVZ), a neural stem cell (NSC) niche, the olfactory bulb (OB), the region where neuronal progenitors differentiate and integrate. These neurogenic zones were compared to the non-neurogenic brain parenchyma of the cerebral cortex. For ultra-deep proteomic assessment of the neurogenic niches, we used library-matched single shot (LMSS) proteomics and identified a total of 10,923 proteins. For proteome–wide assessment of protein compartment and architecture, we used a step-wise tissue de-cellularization protocol, quantitative detergent solubility profiling (QDSP), and identified 8308 proteins. Hence, the data may serve as a basis for future investigation of how unique brain niches allow NSC maintenance and neurogenesis with the final aim to elicit these also in the normal brain parenchyma after neuronal loss.