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

  • Biswapriya B. Misra
Protocol
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 

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

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Biswapriya B. Misra
    • 1
    • 2
  1. 1.Center for Precision Medicine, Section of Molecular Medicine, Department of Internal MedicineWake Forest School of MedicineWinston-SalemUSA
  2. 2.Department of GeneticsTexas Biomedical Research InstituteSan AntonioUSA

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