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Single Cell Metabolism pp 191–217Cite as

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

Part of the Methods in Molecular Biology book series (MIMB,volume 2064)

Abstract

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.

Key words

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

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  • DOI: 10.1007/978-1-4939-9831-9_15
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Abbreviations

CE:

Capillary electrophoresis

DB:

Database

DESI-MS:

Desorption ionization mass spectrometry

GC:

Gas chromatography

GUI:

Graphical user interface

HRMS:

High-resolution mass spectrometry

HRMS/MS:

High-resolution tandem mass spectrometry

KEGG:

Kyoto encyclopedia of genes and genomes

LAESI-MS:

Laser ablation electrospray ionization mass spectrometry

LC:

Liquid chromatography

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

NMR:

Nuclear magnetic resonance

PCA:

Principal component analysis

PLS-DA:

Partial least square -discriminant analysis

QC:

Quality control

QqQ:

Triple quadruple

Q-ToF:

Hybrid quadrupole orthogonal time-of-flight

R:

R-programming language for statistical computing

ToF-MS:

Time-of-flight mass spectrometry

UPLC:

Ultra performance liquid chromatography

XCMS:

Various forms (X) of chromatography mass spectrometry

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Acknowledgements

The author thanks numerous pioneers in mass-spectrometry based metabolomics and single-cell and single cell-type -omics research, the developers and inventors of software tools, resources, and databases in metabolomics research who have inspired this compilation. The author also apologizes to the creators of numerous tools, resources, and analytical innovations that could not find a place in this chapter due to limitation in space or inadvertently.

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Authors and Affiliations

  1. Center for Precision Medicine, Section of Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA

    Biswapriya B. Misra

  2. Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA

    Biswapriya B. Misra

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  1. Biswapriya B. Misra
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  1. Waters Corporation, Milford, MA, USA

    Bindesh Shrestha

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Misra, B.B. (2020). Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics. In: Shrestha, B. (eds) Single Cell Metabolism. Methods in Molecular Biology, vol 2064. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9831-9_15

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  • DOI: https://doi.org/10.1007/978-1-4939-9831-9_15

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