This dataset includes Data-Independent Acquisition (DIA) raw files generated from FFPE medulloblastoma tissue samples collected at NIMHANS, India. Samples were subgrouped into WNT, SHH and non-WNT/non-SHH (NWS) based on immunohistochemical profiling. Deparrafinized tissues were processed using a Filter-Aided Sample Preparation (FASP) protocol, followed by LC-MS/MS analysis on a high-resolution Thermo Scientific Orbitrap Fusion mass spectrometer. DIA acquisition was performed using optimized m/z windows for the samples, and spectral library construction included pooled fraction runs across separate precursor m/z windows. QC pools were run to monitor runwise consistency.