Skip to main content

Mitochondrial Metabolomics Using High-Resolution Fourier-Transform Mass Spectrometry

  • Protocol
  • First Online:
Mass Spectrometry in Metabolomics

Abstract

High-resolution Fourier-transform mass spectrometry (FTMS) provides important advantages in studies of metabolism because more than half of common intermediary metabolites can be measured in 10 min with minimal pre-detector separation and without ion dissociation. This capability allows unprecedented opportunity to study complex metabolic systems, such as mitochondria. Analysis of mouse liver mitochondria using FTMS with liquid chromatography shows that sex and genotypic differences in mitochondrial metabolism can be readily distinguished. Additionally, differences in mitochondrial function are readily measured, and many of the mitochondria-related metabolites are also measurable in plasma. Thus, application of high-resolution mass spectrometry provides an approach for integrated studies of complex metabolic processes of mitochondrial function and dysfunction in disease.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Walberg MW, Clayton DA (1983) In vitro transcription of human mitochondrial DNA. Identification of specific light strand transcripts from the displacement loop region. J Biol Chem 258:1268–1275

    PubMed  CAS  Google Scholar 

  2. Edwards JC, Levens D, Rabinowitz M (1982) Analysis of transcriptional initiation of yeast mitochondrial DNA in a homologous in vitro transcription system. Cell 31:337–346

    Article  PubMed  CAS  Google Scholar 

  3. Ostrander DB, Zhang M, Mileykovskaya E et al (2001) Lack of mitochondrial anionic phospholipids causes an inhibition of translation of protein components of the electron transport chain. A yeast genetic model system for the study of anionic phospholipid function in mitochondria. J Biol Chem 276:25262–25272

    Article  PubMed  CAS  Google Scholar 

  4. Pfisterer J, Buetow DE (1981) In vitro reconstruction of the mitochondrial translation system of yeast. Proc Natl Acad Sci U S A 78:4917–4921

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  5. Chavez JD, Wu J, Bisson W et al (2011) Site-specific proteomic analysis of lipoxidation adducts in cardiac mitochondria reveals chemical diversity of 2-alkenal adduction. J Proteomics 74:2417–2429

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  6. Bhattacharjee A, Majumdar U, Maity D et al (2009) In vivo protein tyrosine nitration in S. cerevisiae: identification of tyrosine-nitrated proteins in mitochondria. Biochem Biophys Res Commun 388:612–617

    Article  PubMed  CAS  Google Scholar 

  7. Ngo JK, Davies KJ (2007) Importance of the lon protease in mitochondrial maintenance and the significance of declining lon in aging. Ann N Y Acad Sci 1119:78–87

    Article  PubMed  CAS  Google Scholar 

  8. Eriksson S, Wang L (2008) Molecular mechanisms of mitochondrial DNA depletion diseases caused by deficiencies in enzymes in purine and pyrimidine metabolism. Nucleosides Nucleotides Nucleic Acids 27:800–808

    Article  PubMed  CAS  Google Scholar 

  9. Sumegi B, Srere PA (1984) Binding of the enzymes of fatty acid beta-oxidation and some related enzymes to pig heart inner mitochondrial membrane. J Biol Chem 259:8748–8752

    PubMed  CAS  Google Scholar 

  10. Christian BE, Spremulli LL (2012) Mechanism of protein biosynthesis in mammalian mitochondria. Biochim Biophys Acta 1819:1035–1054

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  11. Kaminsky YG, Kosenko EA, Kondrashova MN (1982) Metabolites of citric acid cycle, carbohydrate and phosphorus metabolism, and related reactions, redox and phosphorylating states of hepatic tissue, liver mitochondria and cytosol of the pigeon, under normal feeding and natural nocturnal fasting conditions. Comp Biochem Physiol B 73:957–963

    PubMed  CAS  Google Scholar 

  12. Bhuiyan AK, Seccombe D, Bartlett K (1995) Production of acyl-carnitines from the metabolism of [U-14C]3-methyl-2-oxopentanoate by rat liver and skeletal muscle mitochondria. Clin Invest Med 18:144–151

    PubMed  CAS  Google Scholar 

  13. Kunau WH, Dommes V, Schulz H (1995) beta-oxidation of fatty acids in mitochondria, peroxisomes, and bacteria: a century of continued progress. Prog Lipid Res 34:267–342

    Article  PubMed  CAS  Google Scholar 

  14. Miller WL, Auchus RJ (2011) The molecular biology, biochemistry, and physiology of human steroidogenesis and its disorders. Endocr Rev 32:81–151

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  15. Schroepfer GJ Jr (1981) Sterol biosynthesis. Annu Rev Biochem 50:585–621

    Article  PubMed  CAS  Google Scholar 

  16. Sano S, Inoue S, Tanabe Y et al (1959) Significance of mitochondria for porphyrin and heme biosynthesis. Science 129:275–276

    Article  PubMed  CAS  Google Scholar 

  17. Richardson DR, Lane DJ, Becker EM et al (2010) Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol. Proc Natl Acad Sci U S A 107:10775–10782

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  18. Nebert DW, Russell DW (2002) Clinical importance of the cytochromes P450. Lancet 360:1155–1162

    Article  PubMed  CAS  Google Scholar 

  19. Wiseman A, Woods LF (1977) Rapid and economical production of microsomal cytochrome P-450 in yeast resuspended in 20 % glucose medium: relationship to the biosynthesis of mitochondrial cytochromes [proceedings]. Biochem Soc Trans 5:1520–1522

    PubMed  CAS  Google Scholar 

  20. Sato R, Atsuta Y, Imai Y et al (1977) Hepatic mitochondrial cytochrome P-450: isolation and functional characterization. Proc Natl Acad Sci U S A 74:5477–5481

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  21. Aussignargues C, Giuliani MC, Infossi P et al (2012) Rhodanese functions as sulfur supplier for key enzymes in sulfur energy metabolism. J Biol Chem 287:19936–19948

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  22. Roede JR, Park Y, Li S et al (2012) Detailed mitochondrial phenotyping by high resolution metabolomics. PLoS One 7:e33020

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  23. Comisaro MB, Marshall AG (1974) Fourier-transform ion-cyclotron resonance spectroscopy. Chem Phys Lett 25:282–283

    Article  Google Scholar 

  24. Uppal K, Soltow QA, Strobel FH et al (2013) xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data. BMC Bioinform 14:15

    Article  Google Scholar 

  25. Marshall AG, Hendrickson CL (2008) High-resolution mass spectrometers. Annu Rev Anal Chem 1:579–599

    Article  CAS  Google Scholar 

  26. Johnson JM, Strobel FH, Reed M et al (2008) A rapid LC-FTMS method for the analysis of cysteine, cystine and cysteine/cystine steady-state redox potential in human plasma. Clin Chim Acta 396:43–48

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  27. Yu T, Park Y, Johnson JM et al (2009) apLCMS – adaptive processing of high-resolution LC/MS data. Bioinformatics 25:1930–1936

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Scigelova M, Hornshaw M, Giannakopulos A et al (2011) Fourier transform mass spectrometry. Mol Cell Proteomics 10(M111):009431

    PubMed  Google Scholar 

  29. Yu T, Park Y, Li S et al (2013) Hybrid feature detection and information accumulation using high-resolution LC-MS metabolomics data. J Proteome Res 12:1419–1427

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  30. Mayampurath AM, Jaitly N, Purvine SO et al (2008) DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics 24:1021–1023

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  31. Picard M, Taivassalo T, Gouspillou G et al (2011) Mitochondria: isolation, structure and function. J Physiol 589:4413–4421

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  32. Schnaitman C, Greenawalt JW (1968) Enzymatic properties of the inner and outer membranes of rat liver mitochondria. J Cell Biol 38:158–175

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  33. Savage MK, Jones DP, Reed DJ (1991) Calcium- and phosphate-dependent release and loading of glutathione by liver mitochondria. Arch Biochem Biophys 290:51–56

    Article  PubMed  CAS  Google Scholar 

  34. Graham JM (1993) Isolation of mitochondria, mitochondrial membranes, lysosomes, peroxisomes, and Golgi membranes from rat liver. Methods Mol Biol 19:29–40

    PubMed  CAS  Google Scholar 

  35. Dennis EA, Deems RA, Harkewicz R et al (2010) A mouse macrophage lipidome. J Biol Chem 285:39976–39985

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  36. Brown HA, Henage LG, Preininger AM et al (2007) Biochemical analysis of phospholipase D. Methods Enzymol 434:49–87

    Article  PubMed  CAS  Google Scholar 

  37. Johnson JM, Yu T, Strobel FH et al (2010) A practical approach to detect unique metabolic patterns for personalized medicine. Analyst 135:2864–2870

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  38. Soltow QA, Strobel FH, Mansfield KG et al (2013) High-performance metabolic profiling with dual chromatography-Fourier-transform mass spectrometry (DC-FTMS) for study of the exposome. Metabolomics 9:132–143

    Article  CAS  Google Scholar 

  39. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3, Article 3

    Google Scholar 

  40. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (eds) Bioinformatics and computational biology solutions using R and bioconductor. Springer, New York, NY, pp 397–420

    Chapter  Google Scholar 

  41. Lamont LS, Mccullough AJ, Kalhan SC (2003) Gender differences in the regulation of amino acid metabolism. J Appl Physiol 95:1259–1265

    PubMed  CAS  Google Scholar 

  42. Park YH, Lee K, Soltow QA et al (2012) High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring. Toxicology 295:47–55

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  43. Deo RC, Hunter L, Lewis GD et al (2010) Interpreting metabolomic profiles using unbiased pathway models. PLoS Comput Biol 6:e1000692

    Article  PubMed  PubMed Central  Google Scholar 

  44. Pastore A, Federici G, Bertini E et al (2003) Analysis of glutathione: implication in redox and detoxification. Clin Chim Acta 333:19–39

    Article  PubMed  CAS  Google Scholar 

  45. Krishnamurthy PC, Du G, Fukuda Y et al (2006) Identification of a mammalian mitochondrial porphyrin transporter. Nature 443:586–589

    Article  PubMed  CAS  Google Scholar 

  46. Mosser J, Douar AM, Sarde CO et al (1993) Putative X-linked adrenoleukodystrophy gene shares unexpected homology with ABC transporters. Nature 361:726–730

    Article  PubMed  CAS  Google Scholar 

  47. Netik A, Forss-Petter S, Holzinger A et al (1999) Adrenoleukodystrophy-related protein can compensate functionally for adrenoleukodystrophy protein deficiency (X-ALD): implications for therapy. Hum Mol Genet 8:907–913

    Article  PubMed  CAS  Google Scholar 

  48. Momburg F, Roelse J, Howard JC et al (1994) Selectivity of MHC-encoded peptide transporters from human, mouse and rat. Nature 367:648–651

    Article  PubMed  CAS  Google Scholar 

  49. Palmieri F (2004) The mitochondrial transporter family (SLC25): physiological and pathological implications. Pflug Arch Eur J Phys 447:689–709

    Article  CAS  Google Scholar 

  50. Jones DP, Park Y, Ziegler TR (2012) Nutritional metabolomics: progress in addressing complexity in diet and health. Annu Rev Nutr 32:183–202

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  51. Leblanc A, Sleno L (2011) Atrazine metabolite screening in human microsomes: detection of novel reactive metabolites and glutathione adducts by LC-MS. Chem Res Toxicol 24:329–339

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by NIH grants ES009047, ES023485 HL113451, AG038746, ES016731, and NIAID Contract HHSN2722 01200031C.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Dean P. Jones .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Go, YM. et al. (2014). Mitochondrial Metabolomics Using High-Resolution Fourier-Transform Mass Spectrometry. In: Raftery, D. (eds) Mass Spectrometry in Metabolomics. Methods in Molecular Biology, vol 1198. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1258-2_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-1258-2_4

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1257-5

  • Online ISBN: 978-1-4939-1258-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics