Experimental design and reporting standards for metabolomics studies of mammalian cell lines

Abstract

Metabolomics is an analytical technique that investigates the small biochemical molecules present within a biological sample isolated from a plant, animal, or cultured cells. It can be an extremely powerful tool in elucidating the specific metabolic changes within a biological system in response to an environmental challenge such as disease, infection, drugs, or toxins. A historically difficult step in the metabolomics pipeline is in data interpretation to a meaningful biological context, for such high-variability biological samples and in untargeted metabolomics studies that are hypothesis-generating by design. One way to achieve stronger biological context of metabolomic data is via the use of cultured cell models, particularly for mammalian biological systems. The benefits of in vitro metabolomics include a much greater control of external variables and no ethical concerns. The current concerns are with inconsistencies in experimental procedures and level of reporting standards between different studies. This review discusses some of these discrepancies between recent studies, such as metabolite extraction and data normalisation. The aim of this review is to highlight the importance of a standardised experimental approach to any cultured cell metabolomics study and suggests an example procedure fully inclusive of information that should be disclosed in regard to the cell type/s used and their culture conditions. Metabolomics of cultured cells has the potential to uncover previously unknown information about cell biology, functions and response mechanisms, and so the accurate biological interpretation of the data produced and its ability to be compared to other studies should be considered vitally important.

Discrimination of Different Parts of Saffron by Metabolomic‐Based Ultra‐Performance Liquid Chromatography Coupled with High‐Definition Mass Spectrometry

“…Metabolomics (or metabonomics) belong to one of component of systems biology. Recent technological advances have enabled rapid and systematic identification of a large myriad of metabolites or compounds by using sensitive and high‐throughput metabolomic techniques . Metabolomics has the potential to facilitate an understanding and illuminating of the action mechanisms of TCM .…”

“…Recent technological advances have enabled rapid and systematic identification of a large myriad of metabolites or compounds by using sensitive and high-throughput metabolomic techniques. [19][20][21][22][23][24] Metabolomics has the potential to facilitate an understanding and illuminating of the action mechanisms of TCM. [25] Although various mass spectrometry platforms could be used for metabolomics, ultra-performance liquid chromatography coupled with high-definition mass spectrometry (UPLC-HDMS) has been considered to be more suitable for analyzing the metabolite profiling and metabolite identification due to its enhanced reproducibility of retention time.…”

From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data

“…It is vital that the study is designed to maximize useful information, whilst keeping costs and animal usage to a minimum. Ideally, you are aiming for the smallest number of experiments needed to produce the maximum amount of data and achieve precision, whilst addressing power and effect size, and accounting for confounding factors [3]. However, it is challenging to calculate the appropriate sample size for untargeted metabolomics studies, as metabolite changes are typically unknown and may be numerous.…”

Development of an LC-MS Targeted Metabolomics Methodology to Study Proline Metabolism in Mammalian Cell Cultures

“…Metabolomics analysis of cell cultures offers many advantages compared with human and animal metabolomics research, where sometimes the researcher does not have strict control over the number of subjects and the type of samples available for a study. The use of established cell lines, animal or human-sourced, does not involve ethical concerns, which may restrict the number of samples or replicates [ 14 ]. Furthermore, the benefits of cell culture metabolomics include greater control of external variables, greater reproducibility, and easily interpreted results [ 14 , 15 ].…”