Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Abstract

Metabolomics, the large-scale study of the metabolic complement of the cell [1][2][3] , is a mature science that has been practiced for over 20 years 4 . Indeed, it is now a commonly used experimental systems biology tool with demonstrated utility in both fundamental and applied aspects of plant, microbial and mammalian research [5][6][7][8][9][10][11][12][13][14][15] . Among the many thousands of studies published in this area over the last 20 years, notable highlights [5][6][7][8]10,11,16 are briefly described in Supplementary Note 1.Despite the insight afforded by such studies, the nature of metabolites, particularly their diversity (in both chemical structure and dynamic range of abundance 9,12 ), remains a major challenge with regard to the ability to provide adequate coverage of the metabolome that can complement that achieved for the genome, transcriptome and proteome. Despite these comparative limitations, enormous advances have been made with regard to the number of analytes about which accurate quantitative information can be acquired, and a vast number of studies have yielded important biological information and biologically active metabolites across the kingdoms of life 14 . We have previously estimated that upwards of 1 million different metabolites occur across the tree of life, with between 1,000 and 40,000 estimated to occur in a single species 4 .

Applications of Multi-Omics Technologies for Crop Improvement

“…Annotation and reporting of metabolomics data is an important in order to identify and analyze metabolites properly. However, recently, Alseekh et al (2021) reported guidelines for annotation and quantification of LC/GC-MS-based metabolomics data reporting. Their recommended guidelines (i.e., sample preparation, sample replication and randomization, quantification, recovery and recombination, ion suppression, and peak misidentification) could be an effective tool/method for acquisition and reporting of metabolite data.…”

“…Nonetheless, workflow for sampling, quenching, metabolite extraction, and storage has also been elucidated. The adopting certain recommendations may avoid misinterpretation of metabolite data and ensure the reporting transparency in LC/GC-MS-based metabolomics-derived data (Alseekh et al, 2021).…”

Will Casuarina glauca Stress Resilience Be Maintained in the Face of Climate Change?

“…The relative abundance of primary metabolites was normalised considering the FW/dry weight (DW) ratio and the signal intensity of the internal standard (ribitol). Metadata information following the minimum reporting standard guidelines of the Metabolomics Standard Initiative (MSI) [96] can be found in Table S5.…”

“…MS/MS data interpretation was performed by matching the spectra against the METLIN MS/MS (https://metlin.scripps.edu/, last accessed on 12 December 2019) [98], NORMAN MassBank (http://massbank.eu/MassBank/, last accessed on 12 December 2019) and the MoNA (MassBank of North America) (http://mona.fiehnlab.ucdavis.edu/, last accessed on 12 December 2019) high-resolution mass spectral databases. Metadata information following the minimum reporting standard guidelines of the MSI [96] can be found in Table S5.…”

Metabolomics in Retinal Diseases: An Update

“…Each phase consists of numerous steps and key points. For more details, some excellent reviews [6,7] are available. Accurately measuring and unequivocally identifying metabolites are crucial to metabolomics studies.…”