Influence of Drying Method on NMR-Based Metabolic Profiling of Human Cell Lines

Metabolic profiling of cell line and tissue extracts involves sample processing that includes a drying step prior to re-dissolving the cell extracts in a buffer for analysis by GC/LC-MS or NMR. Two of the most commonly used drying techniques are centrifugal evaporation under vacuum and lyophilization. Here, NMR spectroscopy was used to determine how the metabolic profiles of hydrophilic extracts of three human pancreatic cancer cell lines, MiaPaCa-2, Panc-1 and AsPC-1, were influenced by the choice of drying technique. In each of the three cell lines, around forty metabolites were identified to have statistically significant differences in abundance in re-dissolved extract samples depending on the drying technique used during sample preparation. In addition to these differences, some metabolites were only present in lyophilized samples, for example, n-methyl-α-aminoisobutyric acid and ethanol, whereas some metabolites were only present in speed-vacuum dried samples, for example, trimethylamine and n-acetylneuraminic acid. This research demonstrates that the choice of drying technique used during preparation of samples of human cell lines or tissue extracts can significantly influence the observed metabolome making it important to carefully consider the selection of a drying method prior to preparation of such samples for metabolic profiling.