shRNA based PCK2 knockdown was performed in HD-MB03, a Group 3 cell line. Two separate shRNA were used to target PCK2 and empty vector controls. Runs were performed in biological triplicates technical duplicates and in positive and negative ionisation modes. Metabolomics analysis was performed after 72 hours of shRNA induction. QC pools were run in between sample runs to ensure system performance. This data contains all the raw files generated from this analysis.