Application note: Comprehensive cell culture profiling of iPS cells using LCMS Q-TOF – simultaneous analysis of SIM and Scan mode in a single run

In this work we report the metabolic analysis of cell cultures using a high-resolution accurate mass LCMS/MS Q-TOF platform to identify metabolite markers of genomics and phenotypic changes.

Using targeted data acquisition workflow, upregulation (or accumulation) was detected in a number of target amino acids including kynurenine, ornithine and alanine and downregulation (or exhaustion) in the case of tryptophan, arginine and methionine. N’-formylkynurenine was also putatively identified using untargeted data acquisition workflows. 

Developing an optimal cell culture bioprocess for the production of biopharmaceuticals requires routine monitoring of medium conditions such as pH, dissolved gas, carbon source (glucose) and nitrogen source (glutamine). However, cell culture medium is a highly complex mixture, including compounds such as vitamins, amino acids, nucleic acids and other primary metabolites. Metabolite concentrations represent highly sensitive markers to change and help develop a more detailed understanding of the bioprocess. Recently, metabolomics has gained considerable attention for cell culture profiling. In this study, we report comprehensive cell culture profiling of an iPS cell by metabolomics-based LCMS Q-TOF using targeted and untargeted data acquisition workflows.