Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry

Abstract

Advances in liquid chromatography-mass spectrometry (LC-MS) instruments and analytical strategies have brought about great progress in targeted metabolomics analysis. This methodology is now capable of performing precise targeted measurement of dozens or hundreds of metabolites in complex biological samples. Classic targeted quantification assay using the multiple reaction monitoring (MRM) mode has been the foundation of high-quality metabolite quantitation. However, utilization of this strategy in biological studies has been limited by its relatively low metabolite coverage and throughput capacity. A number of methods for large-scale targeted metabolomics assay which have been developed overcome these limitations. These strategies have enabled extended metabolite coverage which is defined as targeting of large numbers of metabolites, while maintaining reliable quantification performance. These recently developed techniques thus bridge the gap between traditional targeted metabolite quantification and untargeted metabolomics profiling, and have proven to be powerful tools for metabolomics study. Although the LC-MRM-MS strategy has been used widely in large-scale metabolomics quantification analysis due to its fast scan speed and ideal analytic stability, there are still drawbacks which are due to the low resolution of the triple quadrupole instruments used for MRM assays. New approaches have been developed to expand the options for large-scale targeted metabolomics study, using high-resolution instruments such as parallel reaction monitoring (PRM). MRM and PRM-based techniques are now attractive strategies for quantitative metabolomics analysis and high-throughput biomarker discovery. Here we provide an overview of the major developments in LC-MS-based strategies for large-scale targeted metabolomics quantification in biological samples. The advantages of LC-MRM/PRM-MS based analytical strategies which may be used in multiplexed and high throughput quantitation for a wide range of metabolites are highlighted. In particular, PRM and MRM strategies are compared, and we summarize the work flow commonly used for large-scale targeted metabolomics analysis including sample preparation, LC separation and data analysis, as well as recent applications in biological studies.

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies

“…Such a strategy allows one to obtain several milliliters of pooled QC extracts. This QC extract is then injected multiple times at regular intervals during instrumental analysis run (e.g., two QC injections every five of eight samples) and algorithms aimed at discarding noisy features or reducing sample-to-sample or batch-to-batch variations in signal intensity from these injections are then applied during data processing [17,[131][132][133][134][135][136][137][138][139][140][141] (see Box 9). High volumes of the extracted pooled QC sample are particularly important when the full sample set is being injected more than once, for example, separately in the positive and negative ionization mode.…”

A Widely Metabolomic Analysis Revealed Metabolic Alterations of Epimedium Pubescens Leaves at Different Growth Stages

“…However, it had an overall better precision in compound identification than the untargeted metabolomics method [17]. In addition, the metabolite coverage and throughput of targeted metabolomics analysis was greatly enhanced with the recent breakthroughs of LC-MS based large-scale targeted metabolomics methodologies and also with the MS/MS library databases constructed and enriched [18][19][20]. Following the widely targeted metabolomics method that Chen et al developed in 2013 [18], 661 metabolites in Chrysanthemum morifolium.…”

Endogenous and xenobiotic metabolic stability of primary human hepatocytes in long‐term 3D spheroid cultures revealed by a combination of targeted and untargeted metabolomics

“…Yet, their metabolomic signatures have not been investigated. Liquid chromatography in combination with single or tandem mass spectrometry has been used for measuring in vitro cytochrome P450 (CYP) activity, as well as for targeted and untargeted metabolomics (25, 26). For quantification purposes, this technique requires the predefinition of analytes of interest through parameter optimization.…”