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Glioblastoma (GBM) cancer stem cells (GSCs) contribute to GBM's origin, recurrence, and resistance to treatment. However, understanding how mRNA expression patterns of GBM subtypes are reflected at the global proteome level in GSCs is limited. To characterize protein expression in GSCs, we performed an in‐depth proteogenomic analysis of patient‐derived GSCs by RNA sequencing and mass‐spectrometry. In summary, GSCs express two protein sets that have an inverse association with clinical outcomes in GBM. In addition, the discovery of non‐canonical protein sequences questions existing gene models and pinpoints new protein targets for research in GBM.
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