Metabolomic profile of pancreatic cancer cell co-cultures with pancreatic cystic tumour associated-bacterial strains

The dataset is tied to a manuscript titled "Patient-derived pancreatic tumor bacteria induce oncogenic aberrations in pancreatic spheroids and are recognized by MAIT cells" by Poojabahen et al., submitted to Gut Microbes (Ref: KGMI-20230959) and currently in revision.

Pancreatic cancer cell lines (AsPC-1, Capan-2), as well as a non-cancer immortalised pancreatic cell line (hTERT-HPNE) were infected with a panel of live bacterial isolates derived from pancreatic cystic tumours at MOI 1 for 24h. Culture supernatants were frozen at -80C at collection and later analysed using mass spectrometry-based metabolomics, as follows:

Supernatant aliquots were thawed on ice then a 10 mL aliquot was diluted with 240 mL of cold 5:3:2 methanol:acetonitrile:water (v/v/v) and vortexed for 30 min at 4C. Supernatants were clarified (10,000 × g, 10 min, 4C) and then analyzed via 20 mL injections on a Thermo Vanquish UHPLC coupled to a Thermo Q Exactive mass spectrometer operating in positive and negative ion modes (separate runs) with a 5 min C18 gradient. Raw files were converted to mzXML using RawConverter, and metabolites were annotated and integrated in Maven using the KEGG database.