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Structural Mass Spectrometry for Metabolomics

  • Richard M. HigashiEmail author
Protocol
Part of the Methods in Pharmacology and Toxicology book series (MIPT)

Abstract

Structural mass spectrometry (MS) is a chemical structure-revealing analytical technique that measures mass/charge ratio of ions. Biochemical analyses in the context of metabolomics—which seeks chemical descriptions of cellular, organismal, and even community biology—pose challenges distinct from past applications of MS. The scientific need for both far greater depth and breadth of metabolic analytes is manifested analytically in two general approaches: the “Biomarker” approach and the “Pathway” approach. In this chapter, the basic principles of mass spectrometry relevant to these two approaches to metabolomics are reviewed. The emphasis is on practical aspects of how experimental design interacts with instrument designs and capabilities. Both simulated theoretical and real-life analyses are used to illustrate the key concepts and their ramifications.

Key words

High resolution MS Stable isotope resolved metabolomics Isotopologue analysis Metabolic pathways 

Abbreviations

ddMSn

Data-dependent MSn

FT-ICR

Fourier transform ion cyclotron resonance

GC

Gas chromatography

HIT

High information throughput

ICP-MS

Inductively coupled plasma MS

IR

Infrared

LC

Liquid chromatography

MDLs

Minimum detectable limits

MQLs

Minimum quantifiable limits

MRM

Multiple reaction monitoring

MS

Mass spectrometry

MS2

MS to the 2nd or tandem MS

MSn

MS to the nth

NA

Natural abundance

NMR

Nuclear magnetic resonance spectroscopy

PC

Phosphatidylcholine

RF

Radio frequency

SIRM

Stable isotope-resolved metabolomics

ToF

Time of flight

UV

Ultraviolet visible

Notes

Acknowledgments

The unpublished data shown here was supported in part by grants from NSF EPSCoR EPS-0447479, NIH 1R01CA118434-01A2, NCI R21CA133688, and the Susan G. Komen Foundation BCTR0503648 while the published data was supported by the grants listed in the cited publications. The author thanks T. Fan, A.N. Lane, H, Moseley, J. Winiike, P. Lorkiewicz, M. Arita, J. Goran, and T. Cassel, among numerous others, for helpful discussions.

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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Department of Chemistry, Center for Regulatory and Environmental Analytical Metabolomics (CREAM), and James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleUSA

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