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.
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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
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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The unpublished data shown here was supported in part by grants from NSF EPSCoR EPS-0447479, NIH 1R01CA118434-01A2, NCI R21CA133688, and the Susan G. Komen Foundation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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Higashi, R.M. (2012). Structural Mass Spectrometry for Metabolomics. In: Fan, TM., Lane, A., Higashi, R. (eds) The Handbook of Metabolomics. Methods in Pharmacology and Toxicology. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-618-0_4
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DOI: https://doi.org/10.1007/978-1-61779-618-0_4
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