Skip to main content

Isotopic Distributions

  • Protocol
  • First Online:
Mass Spectrometry Data Analysis in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2051))

Abstract

Isotopic information determined by mass spectrometry can be used in a wide variety of applications. Broadly speaking these could be classified as “passive” applications, meaning that they use naturally occurring isotopic information, and “active” applications, meaning that the isotopic distributions are manipulated in some way. The classic passive application is the determination of chemical composition by comparing observed isotopic patterns of molecules to theoretically calculated isotopic patterns. Active applications include isotope exchange experiments of a variety of types, as well as isotope labeling in tracing studies and to provide references for quantitation. Regardless of the type of application considered, the problem of theoretical calculation of isotopic patterns almost invariably arises. This chapter reviews a number of application examples and computational approaches for isotopic studies in mass spectrometry.

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 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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

Similar content being viewed by others

References

  1. Reimer PJ et al (2009) IntCal09 and Marine09 radiocarbon age calibration curves, 0–50,000 years cal BP. Radiocarbon 51(4):1111–1150

    Article  CAS  Google Scholar 

  2. de Laeter JR (1998) Mass spectrometry and geochronology. Mass Spectrom Rev 17(2):97–125

    Article  Google Scholar 

  3. Kreuzer-Martin HW, Jarman KH (2007) Stable isotope ratios and forensic analysis of microorganisms. Appl Environ Microbiol 73(12):3896–3908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. McDermott F (2004) Palaeo-climate reconstruction from stable isotope variations in speleothems: a review. Q Sci Rev 23(7–8):901–918

    Article  Google Scholar 

  5. Harris SB et al (2012) List of observationally-stable isotopes. Available from: http://en.wikipedia.org/wiki/Stable_isotope#List_of_observationally-stable_isotopes

  6. Yergey JA (1983) A general approach to calculating isotopic distributions for mass Spectrometry. Int J Mass Spectrom Ion Phys 52:337–349

    Article  CAS  Google Scholar 

  7. Hsu CS (1984) Diophantine approach to isotopic abundance calculations. Anal Chem 56(8):1356–1361

    Article  CAS  Google Scholar 

  8. Rockwood AL, VanOrden SL, Smith RD (1996) Ultrahigh resolution isotope distribution calculations. Rapid Commun Mass Spectrom 10(1):54–59

    Article  CAS  Google Scholar 

  9. Kubinyi H (1991) Calculation of isotope distributions in mass spectrometry. A trivial solution for a non-trivial problem. Anal Chim Acta 247:107–119

    Article  CAS  Google Scholar 

  10. Rockwood AL, Van Orden SL (1996) Ultrahigh-speed calculation of isotope distributions. Anal Chem 68:2027–2030

    Article  CAS  PubMed  Google Scholar 

  11. Rockwood AL, Van Orman JR, Dearden DV (2004) Isotopic compositions and accurate masses of single isotopic peaks. J Am Soc Mass Spectrom 15(1):12–21

    Article  CAS  PubMed  Google Scholar 

  12. Roussis SG, Proulx R (2003) Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra. Anal Chem 75(6):1470–1482

    Article  CAS  PubMed  Google Scholar 

  13. Rockwood AL, Haimi P (2006) Efficient calculation of accurate masses of isotopic peaks. J Am Soc Mass Spectrom 17(3):415–419

    Article  CAS  PubMed  Google Scholar 

  14. Arfken G (1985) Convolution theorem §15.5, in mathematical methods for physicists. Academic Press, Orlando, FL

    Google Scholar 

  15. Cooley JW, Tukey JW (1965) An algorithm for the machine calculation of complex Fourier series. Math Comput 19:297–301

    Article  Google Scholar 

  16. Rockwood AL (1995) Relationship of Fourier transforms to isotope distribution calculations. Rapid Commun Mass Spectrom 9:103–105

    Article  CAS  Google Scholar 

  17. Rockwood AL, Van Orden SL, Smith RD (1995) Rapid calculation of isotope distributions. Anal Chem 67:2699–2704

    Article  CAS  Google Scholar 

  18. Frigo M, Johnson SG (1998) FFTW: an adaptive software architecture for the FFT. In: The IEEE international conference on acoustics, speech and signal processing, Seattle

    Google Scholar 

  19. GSL—GNU scientific library (2007)

    Google Scholar 

  20. Valkenborg D et al (2012) The isotopic distribution conundrum. Mass Spectrom Rev 31(1):96–109

    Article  CAS  PubMed  Google Scholar 

  21. Claesen J et al (2012) An efficient method to calculate the aggregated isotopic distribution and exact center-masses. J Am Soc Mass Spectrom 23(4):753–763

    Article  CAS  PubMed  Google Scholar 

  22. Palmblad M, Buijs J, Håkansson P (2001) Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions. J Am Soc Mass Spectrom 12(11):1153–1162

    Article  CAS  PubMed  Google Scholar 

  23. Palmblad M, Mills DJ, Bindschedler LV (2008) Heat-shock response in Arabidopsis thaliana explored by multiplexed quantitative proteomics using differential metabolic labeling. J Proteome Res 7(2):780–785

    Article  CAS  PubMed  Google Scholar 

  24. Tou JC, Zakett D, Caldecourt VJ (1983) Tandem mass spectrometry of industrial chemicals. In: McLafferty FW (ed) Tandem mass spectrometry. John Wiley and Sons, New York, pp 441–446

    Google Scholar 

  25. Rockwood AL, Kushnir MM, Nelson GJ (2003) Dissociation of individual isotopic peaks: predicting isotopic distributions of product ions in MSn. J Am Soc Mass Spectrom 14(4):311–322

    Article  CAS  PubMed  Google Scholar 

  26. Beynon J (ed) (1960) Mass spectrometry and its applications to organic chemistry. Elsevier Science, Amsterdam, pp 294–302

    Google Scholar 

  27. Zemany PD (1950) Punched card catalog of mass spectra useful in qualitative analysis. Anal Chem 22(7):920–922

    Article  CAS  Google Scholar 

  28. Kind T, Fiehn O (2007) Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8:105

    Article  PubMed  PubMed Central  Google Scholar 

  29. Wang Y, Gu M (2010) The concept of spectral accuracy for MS. Anal Chem 82(17):7055–7062

    Article  CAS  PubMed  Google Scholar 

  30. Erve JCL et al (2009) Spectral accuracy of molecular ions in an LTQ/Orbitrap mass spectrometer and implications for elemental composition determination. J Am Soc Mass Spectrom 20(11):2058–2069

    Article  CAS  PubMed  Google Scholar 

  31. Todd PJ, Barbalas MP, Mclafferty FW (1982) Collisional activation mass-spectra of ions containing polyisotopic elements. Org Mass Spectrom 17(2):79–80

    Article  CAS  Google Scholar 

  32. Software for Mass Spectrometry (2012) [cited 2012 20120509]. Available from: http://tarc.chemistry.dal.ca/soft_down.htm

  33. Tsutsui Y, Wintrode PL (2007) Hydrogen/deuterium, exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Curr Med Chem 14(22):2344–2358

    Article  CAS  PubMed  Google Scholar 

  34. Palmblad M (2000) AUTOHD [cited 2012]. Available from: http://www.ms-utils.org/autohd.html

  35. Hotchko M et al (2006) Automated extraction of backbone deuteration levels from amide H/(2) H mass spectrometry experiments. Protein Sci 15(3):583–601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Pascal BD et al (2009) HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J Am Soc Mass Spectrom 20(4):601–610

    Article  CAS  PubMed  Google Scholar 

  37. Whitelegge JP et al (2004) Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics. Phytochemistry 65(11):1507–1515

    Article  CAS  PubMed  Google Scholar 

  38. Palmblad M (2007) muxQuant [cited 2012]. Available from: http://ms-utils.org/muxQuant

  39. Kirchner M et al (2011) Changing the rules of the game: next generation quantification (NGQ) enables complete isotopic multiplexing for quantitative functional and dynamic proteomics. In: 59th ASMS conference on mass spectrometry and allied topics, Denver, CO.

    Google Scholar 

  40. Ong SE et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376–386

    Article  CAS  PubMed  Google Scholar 

  41. Ross PL et al (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154–1169

    Article  CAS  PubMed  Google Scholar 

  42. Horn DM, Zubarev RA, McLafferty FW (2000) Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom 11(4):320–332

    Article  CAS  PubMed  Google Scholar 

  43. Fernandez-de-Cossio Diaz J, Fernandez-de-Cossio J (2012) Computation of isotopic peak center-mass distribution by Fourier transform. Anal Chem 84(16):7052–7056

    Article  CAS  PubMed  Google Scholar 

  44. Schwartz JC, Zhou X-G, Bier ME (1996) Method and apparatus of increasing dynamic range and sensitivity of a mass spectrometer. US

    Google Scholar 

  45. Element 114 is named flerovium and element 116 is named Livermorium (2012). Available from: http://www.iupac.org/news/news-detail/article/element-114-is-named-flerovium-and-element-116-is-named-livermorium.html

  46. de Marcillac P et al (2003) Experimental detection of alpha-particles from the radioactive decay of natural bismuth. Nature 422(6934):876–878

    Article  PubMed  Google Scholar 

  47. Wan KX, Vidavsky I, Gross ML (2002) Comparing similar spectra: from similarity index to spectral contrast angle. J Am Soc Mass Spectrom 13(1):85–88

    Article  CAS  PubMed  Google Scholar 

  48. Fernandez-de-Cossio J (2010) Efficient packing Fourier-transform approach for ultrahigh resolution isotopic distribution calculations. Anal Chem 82(5):1759–1765

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Magnus Palmblad .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

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

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Rockwood, A.L., Palmblad, M. (2020). Isotopic Distributions. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9744-2_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9744-2_3

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9743-5

  • Online ISBN: 978-1-4939-9744-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics