Skip to main content
SpringerLink
Log in

The Analysis of Peptide-Centric Mass-Spectrometry Data Utilizing Information About the Expected Isotope Distribution

  • Chapter
  • First Online:
Book cover Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

Part of the book series: Frontiers in Probability and the Statistical Sciences ((FROPROSTAS))

Abstract

In shotgun proteomics, much attention and instrument time is dedicated to the generation of tandem mass spectra. These spectra contain information about the fragments of, ideally, one peptide and are used to infer the amino acid sequence of the scrutinized peptide. This type of spectrum acquisition is called a product ion scan, tandem MS, or MS2 spectrum. Another type of spectrum is the, often overlooked, precursor ion scan or MS1 spectrum that catalogs all ionized analytes present in a mass spectrometer. While MS2 spectra are important to identify the peptides and proteins in the sample, MS1 spectra provide valuable information about the quantity of the analyte. In this chapter, we describe some properties of MS1 spectra, such as the isotope distribution, and how these properties can be employed for low-level signal processing to reduce data complexity and as a tool for quality assurance. Furthermore, we describe some cases in which advanced modeling of the isotope distribution can be used in quantitative proteomics analysis.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
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

References

  1. Atlas, M., & Datta, S. (2009). A statistical technique for monoisotopic peak detection in a mass spectrum. Journal of Proteomics and Bioinformatics, 2, 202–216.

    Article  Google Scholar 

  2. Claesen, J., Dittwald, P., Burzykowski, T., & Valkenborg, D. (2012). An efficient method to calculate the aggregated isotopic distribution and exact center-masses. Journal fo the American Society for Mass Spectrometry, 23, 753–763.

    Article  Google Scholar 

  3. Eckel-Passow, J. E., Oberg, A. L., Therneau, T. M., Mason, C. J., Mahoney, D. W., Johnson, K. L., et al. (2006). Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass-spectrometry. Bioinformatics, 2, 305–318.

    Google Scholar 

  4. Geller, O., & Lifshitz, C. (2004). Applying a new algorithm to H/D exchange of multiply protonated cytochrome c. International Journal of Mass Spectrometry, 223, 125–129.

    Article  Google Scholar 

  5. Gevaert, K., Impens, F., Ghesquière, B., Van Damme, P., Lambrechts, A., & Vandekerckhove, J. (2008). Stable isotopic labeling in proteomics. Proteomics, 8, 4873–4885.

    Article  Google Scholar 

  6. Ghavidel, F. Z., Mertens, I., Baggerman, G., Laukens, K., Burzykowski, T., & Valkenborg, D. (2014). The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results. Journal of Proteomics, 98, 150–158.

    Article  Google Scholar 

  7. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnology, 17, 994–999.

    Article  Google Scholar 

  8. Impens, F., Colaert, N., Helsens, K., Ghesquière, B., Timmerman, E., De Bock, P. J., et al. (2010). A quantitative proteomics design for systematic identification of protease cleavage events. Molecular and Cellular Proteomics, 9, 2327–2333.

    Article  Google Scholar 

  9. Lermyte, F., Konijnenberg, A., Williams, J. P., Brown, J. M., Valkenborg, D., & Sobott, F. (2014). ETD allows for native surface mapping of a 150 kDa noncovalent complex on a commercial Q-TWIMS-TOF instrument. Journal of the American Society for Mass Spectrometry, 25, 343–350.

    Article  Google Scholar 

  10. Lermyte, F., Verschueren, T., Brown, J. M., Williams, J. P., Valkenborg, D., & Sobott, F. (2015). Characterization of top-down ETD in a travelling-wave ion guide. Methods, 89, 22–29.

    Google Scholar 

  11. Lermyte, F., Łąckic, M. K., Valkenborg, D., Baggerman, G., Gambin, A., & Sobott, F. (2015). Understanding reaction pathways in top-down ETD by dissecting isotope distributions: A mammoth task. International Journal of Mass Spectrometry, 390, 146–154.

    Google Scholar 

  12. Lopez-Ferrer, D., Ramos-Fernandez, A., Martinez-Bartolome, S., Garca-Ruiz, P., & Vazquez, J. (2006). Quantitative proteomics using 16O/18O labeling and linear ion trap mass spectrometry. Proteomics, 6, S4–S11.

    Article  Google Scholar 

  13. Mirgorodskaya, O. A., Kozmin, Y. P., Titov, M. I., Korner, R., Sonksen, C. P., & Roepstorff, P. (2000). Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using 18O-labeled internal standards. Rapid Communications in Mass Spectrometry, 14, 1226–1232.

    Article  Google Scholar 

  14. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., et al. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular and Cellular Proteomics, 1, 376–386.

    Article  Google Scholar 

  15. Palmblad, M., Buijs, J., & Hakansson, P. (2001). Automatic analysis of Hydrogen/Deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions. Journal of the American Society for Mass Spectrometry, 12, 1153–1162.

    Article  Google Scholar 

  16. Park, S. K., Jin, L. L., Kim, Y., & Yates, J. R., III. (2009). A computational approach to correct arginine-to-proline conversion in quantitative proteomics. Nature Methods, 6, 184–185.

    Article  Google Scholar 

  17. Rao, K. C., Carruth, R. T., & Miyagi, M. (2005). Proteolytic 18O-labeling by peptidyl-Lys metalloendopeptidase for comparative proteomics. Journal of Proteome Research, 4, 507–514.

    Article  Google Scholar 

  18. Reuben, B., Ritov, Y., Geller, O., McFarland, M., Marshall, A., & Lifshitz, C. (1993). Applying a new algorithm for obtaining site specific rate constants for H/D exchange of the gas phase proton-bound arginine dimer. Chemical Physics Letters, 380, 88–94.

    Article  Google Scholar 

  19. Rockwood, A. L., & Van Orden, S. L. (1996). Ultrahigh-speed calculation of isotope distributions. Analytical Chemistry, 68, 2027–2030.

    Article  Google Scholar 

  20. Rosman, K. J. R., & Taylor, P. D. P. (1998). Isotopic compositions of the elements 1997. Pure and Applied Chemistry, 70, 217–235.

    Article  Google Scholar 

  21. Schmidt, A., Kellermann, J., & Lottspeich, F. (2005). A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics, 5, 4–15.

    Article  Google Scholar 

  22. Senko, M. W., Beu, S. C., & McLafferty, F. W. (1995). Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distribution. Journal of the American Society for Mass Spectrometry, 6, 229–233.

    Article  Google Scholar 

  23. Shadforth, I. P., Dunkley, T. P. J., Lilley, K. S., & Bessant, C. (2005). i-Tracker: For quantitative proteomics using iTRAQ™. BMC Genomics, 6, 145.

    Google Scholar 

  24. Smith, D., Deng, Y., & Zhang, Z. (1997). Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. Journal of Mass Spectrometry, 32, 135–146.

    Article  Google Scholar 

  25. Stemmann, O., Zou, H., Gerber, S. A., Gygi, S. P., & Kirschner, M. W. (2001). Dual inhibition of sister chromatid separation at metaphase. Cell, 107, 715–726.

    Article  Google Scholar 

  26. Valkenborg, D., Jansen, I., & Burzykowski, T. (2008). A model-based method for the prediction of the isotopic distribution of peptides. Journal of the American Society for Mass Spectrometry, 19, 703–712.

    Article  Google Scholar 

  27. Valkenborg, D., & Burzykowski, T. (2011). A Markov-chain model for the analysis of high-resolution enzymatically 18O-labeled mass spectra. Statistical Applications in Genetics and Molecular Biology, 10, article 1.

    Google Scholar 

  28. Valkenborg, D., Mertens, I., Lemière, F., Witters, E., & Burzykowski, T. (2012). The isotopic distribution conundrum. Mass Spectrometry Reviews, 31, 96–109.

    Article  Google Scholar 

  29. Zhang, Z., & Smith, D. L. (1993). Determination of amide Hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation. Protein Science, 2, 522–531.

    Article  Google Scholar 

  30. Zhang, Z., Guan, S., & Marshall, A. (1997). Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum-entropy based deconvolution to eliminate the isotopic natural abundance distribution. Journal of the American Society for Mass Spectrometry, 8, 659–670.

    Article  Google Scholar 

  31. Zhu, Q., & Burzykowski, T. (2011). A Bayesian Markov-chain-based heteroscedastic regression model for the analysis of 18O-labelled mass spectra. Journal of the American Society for Mass Spectrometry, 22, 499–507.

    Article  Google Scholar 

  32. Zhu, Q., Valkenborg, D., & Burzykowski, T. (2010). A Markov-chain-based heteroscedastic regression model for the analysis of high-resolution enzymatically 18O-labeled mass spectra. Journal of Proteome Research, 9, 2669–2677.

    Article  Google Scholar 

  33. Ye, X., Luke, B., Andresson, T., & Blonder, J. (2009). 18O stable isotope labeling in MS-based proteomics. Briefings in Functional Genomics and Proteomics, 8, 136–144.

    Article  Google Scholar 

  34. Zhu, Q., Kasim, A., Valkenborg, D., & Burzykowski, T. (2011). A Bayesian model-averaging approach to the quantification of overlapping peptides in a MALDI-TOF mass spectrum. International Journal of Proteomics, article ID 928391.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. I-BioStat, Hasselt University, Diepenbeek, Belgium

    Tomasz Burzykowski, Jürgen Claesen & Dirk Valkenborg

  2. IDDI, Louvain-la-Neuve, Belgium

    Tomasz Burzykowski

  3. VITO, Mol, Belgium

    Dirk Valkenborg

  4. Center for Proteomics, University of Antwerp, Antwerp, Belgium

    Dirk Valkenborg

Authors
  1. Tomasz Burzykowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jürgen Claesen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dirk Valkenborg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tomasz Burzykowski .

Editor information

Editors and Affiliations

  1. Department of Biostatistics, University of Florida, Gainesville, Florida, USA

    Susmita Datta

  2. Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, RC Leiden, The Netherlands

    Bart J. A. Mertens

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Burzykowski, T., Claesen, J., Valkenborg, D. (2017). The Analysis of Peptide-Centric Mass-Spectrometry Data Utilizing Information About the Expected Isotope Distribution. In: Datta, S., Mertens, B. (eds) Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry. Frontiers in Probability and the Statistical Sciences. Springer, Cham. https://doi.org/10.1007/978-3-319-45809-0_3

Download citation

Publish with us

Policies and ethics

Search

Navigation