A LC–MS/MS platform for the identification of productivity markers in industrial mammalian cell culture media

Abstract

Abstract Cell culture media formulations supplemented with soy hydrolysates for commercial scale manufacturing of therapeutic proteins were characterized by high-resolution LC–MS/MS to identify specific media components that contributed to cellular bioprocess variability. Initial untargeted screening of media formulations resulted in the combined quantification of >2500 features upon analysis by reversed-phase and hydrophilic interaction liquid chromatography. Chemometric evaluation of quantified features by Principal Component Analysis and Hierarchical Clustering revealed clear correlation between media lots and the corresponding hydrolysates implemented during formulation development stages, suggesting that the observed variation in culture performance could be influenced by components present within hydrolysates. Through multivariate data analysis, a small number of dipeptides, identified as Tyrosyl-Leucine, Phenylalanyl-Valine and LL-Cyclo(Leucylprolyl) were determined in media as potential contributors to bioprocess variability due to their statistically significant higher abundance in formulations which yielded low cellular productivity. Subsequent quantification of these features was performed through targeted LC-QQQ-MS/MS which however, revealed discrepancies between dipeptide concentration levels in media and corresponding hydrolysates presumably due to their potential instability upon interaction with other chemically defined components such as metals or chelating agents. The nutritional impact of the aforementioned features of interest on CHO cell growth performance was assessed through spiking studies in representative shake-flask cultures which however, failed to demonstrate clear correlation between dipeptide concentrations and achieved product yields further indicating the presence of a plausible synergetic effect between the identified dipeptides and alternative media components.