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Methods Mol Biol. 2020;2064:191-217. doi: 10.1007/978-1-4939-9831-9_15.

Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics.

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Center for Precision Medicine, Section of Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA.
Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA.


In this age of -omics data-guided big data revolution, metabolomics has received significant attention as compared to genomics, transcriptomics, and proteomics for its proximity to the phenotype, the promises it makes and the challenges it throws. Although metabolomes of entire organisms, organs, biofluids, and tissues are of immense interest, a cell-specific resolution is deemed critical for biomedical applications where a granular understanding of cellular metabolism at cell-type and subcellular resolution is desirable. Mass spectrometry (MS) is a versatile technique that is used to analyze a broad range of compounds from different species and cell-types, with high accuracy, resolution, sensitivity, selectivity, and fast data acquisition speeds. With recent advances in MS and spectroscopy-based platforms, the research community is able to generate high-throughput data sets from single cells. However, it is challenging to handle, store, process, analyze, and interpret data in a routine manner. In this treatise, I present a workflow of metabolomics data generation from single cells and single-cell types to their analysis, visualization, and interpretation for obtaining biological insights.


Analysis; Animal; Cell; Computational; Data; Database; Mass spectrometry; Metabolomics; Microbial; Network; Pathway; Plant; Single cell; Single-cell type; Software; Statistical; Tool; Web server; –Omics

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