Comparison of liquid chromatography-mass spectrometry and direct infusion microchip electrospray ionization mass spectrometry in global metabolomics of cell samples

In this study, the feasibility of direct infusion electrospray ionization microchip mass spectrometry (chip-MS) was compared to the commonly used liquid chromatography-mass spectrometry (LC-MS) in non-targeted metabolomics analysis of human foreskin fibroblasts (HFF) and human induced pluripotent stem cells (hiPSC) reprogrammed from HFF. The total number of the detected features with chip-MS and LC-MS were 619 and 1959, respectively. Approximately 25% of detected features showed statistically significant changes between the cell lines with both analytical methods. The results show that chip-MS is a rapid and simple method that allows high sample throughput from small sample volumes and can detect the main metabolites and classify cells based on their metabolic profiles. However, the selectivity of chip-MS is limited compared to LC-MS and chip-MS may suffer from ion suppression.