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Comparison of the Mahalanobis Distance and Pearson’s χ2 Statistic as Measures of Similarity of Isotope Patterns

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Journal of The American Society for Mass Spectrometry

Abstract

To extract a genuine peptide signal from a mass spectrum, an observed series of peaks at a particular mass can be compared with the isotope distribution expected for a peptide of that mass. To decide whether the observed series of peaks is similar to the isotope distribution, a similarity measure is needed. In this short communication, we investigate whether the Mahalanobis distance could be an alternative measure for the commonly employed Pearson’s χ2 statistic. We evaluate the performance of the two measures by using a controlled MALDI-TOF experiment. The results indicate that Pearson’s χ2 statistic has better discriminatory performance than the Mahalanobis distance and is a more robust measure.

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References

  1. Valkenborg, D., Mertens, I., Lemière, F., Witters, F., Burzykowski, T.: The isotopic distribution conundrum. Mass Spectrom. Rev. 31(1), 96–109 (2011)

    Article  Google Scholar 

  2. Rockwood, A.L., Palmblad, M.: Isotopic distributions. Methods Mol. Biol. 1007, 65–99 (2013)

    Article  CAS  Google Scholar 

  3. Renard, B.Y., Kirchner, M., Steen, H., Steen, J.A.J., Hamprech, F.A.: NITPICK: Peak identification for mass spectrometry data. BMC Bioinforma 9, 355 (2008)

    Article  Google Scholar 

  4. Nicolardi, S., Palmblad, M., Dalebout, H., Bladergroen, M., Tollenaar, R.A., Deelder, A.M., van der Burgt, Y.E.: Quality control based on isotopic distributions for high-throughput MALDI-TOF and MALDI-FTICR serum peptide profiling. J. Am. Soc. Mass Spectrom. 21(9), 1515–1525 (2010)

    Article  CAS  Google Scholar 

  5. Senko, M.W., Beu, S.C., McLafferty, F.W.: Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distribution. J. Am. Soc. Mass Spectrom. 6, 229–233 (2005)

    Article  Google Scholar 

  6. Hsieh, E.J., Hoopmann, M.R., Maclean, B., MacCoss, M.J.: Comparison of database search strategies for high precursor mass accuracy MS/MS data. J. Proteome Res. 9(2), 1138–1143 (2010)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Valkenborg, D., Assam, P., Thomas, G., Krols, L., Kas, K., Burzykowski, T.: Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach. Rapid Commun. Mass Spectrom. 21, 3387–3391 (2007)

    Article  CAS  Google Scholar 

  9. Valkenborg, D., Thomas, G., Krols, L., Kas, K., Burzykowski, T.: A strategy to analyse data from high performance liquid chromatography combined with high resolution mass spectrometry. J. Mass Spectrom. 44, 516–529 (2009)

    Article  CAS  Google Scholar 

  10. Senko, M.W., Beu, S.C., McLafferty, F.W.: Automated assignment of charge states from resolved isotopic peaks for multiply-charged ions. J. Am. Soc. Mass Spectrom. 6, 52–56 (1995)

    Article  CAS  Google Scholar 

  11. Breen, E.J., Hopwood, F.G., Williams, K.L., Wilkins, M.R.: Automatic poisson peak harvesting for high throughput protein identification. Electrophoresis 21, 2243–2251 (2000)

    Article  CAS  Google Scholar 

  12. Gay, S., Binz, P.A., Hochstrasser, D.F., Appel, R.D.: Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis 20, 3527–3534 (1999)

    Article  CAS  Google Scholar 

  13. Mahalanobis, P.C.: On the generalized distance in statistics. Proc. Natl. Inst. Sci. India 2(1), 49–55 (1936)

    Google Scholar 

  14. Matzke, M.M., Waters, K.M., Metz, T.O., Jacobs, J.M., Sims, A.C., Baric, R.S., Pounds, J.G., Webb-Robertson, B.J.: Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics 27(20), 2866–2872 (2011)

    Article  CAS  Google Scholar 

  15. Schulz-Trieglaff, O., Machtejevas, E., Reinert, K., Schlüter, H., Thiemann, J., Unger, K.: Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioDataMining 2(1) Article 4 (2009)

    Google Scholar 

  16. Cairns, D.A., Perkins, D.N., Stanley, A.J., Thompson, D., Barrett, J.H., Selby, P.J., Banks, R.E.: Integrated multi-level quality control for proteomic profiling studies using mass spectrometry. BMC Bioinforma 9, 519 (2008)

    Article  Google Scholar 

  17. Liu, Q., Sung, A.H., Qiao, M., Chen, Z., Yang, J.Y., Yang, M.Q., Huang, X., Deng, Y.: Comparison of feature selection and classification for MALDI-MS data. BMC Genomics 10(Suppl 1), S3 (2009)

    Article  Google Scholar 

  18. Picotti, P., Aebersold, R., Domon, B.: The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics 6(9), 1589–1598 (2007)

    Article  CAS  Google Scholar 

  19. Valkenborg, D., Jansen, I., Burzykowski, T.: A model-based method for the prediction of the isotopic distribution of peptides. J. Am. Soc. Mass Spectrom. 19(5), 703–712 (2008)

    Article  CAS  Google Scholar 

  20. Dittwald, P., Valkenborg, D., Claesen, J., Burzykowski, T., Gambin, A.: BRAIN: A universal tool for high-throughput calculations of isotopic distribution for mass spectrometry. Anal. Chem. 85(4), 1991–1994 (2013)

    Article  CAS  Google Scholar 

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Acknowledgments

D.V. acknowledges the support of the SBO grant ‘InSPECtor’ (120025) of the Flemish agency for Innovation by Science and Technology (IWT).

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Authors and Affiliations

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

    Fatemeh Zamanzad Ghavidel, Jürgen Claesen, Tomasz Burzykowski & Dirk Valkenborg

  2. Applied Bio and Molecular Systems, Flemish Institute for Technological Research, VITO, Mol, Belgium

    Dirk Valkenborg

  3. Center for Proteomics, Antwerp, Belgium

    Dirk Valkenborg

Authors
  1. Fatemeh Zamanzad Ghavidel
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  2. Jürgen Claesen
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  3. Tomasz Burzykowski
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  4. Dirk Valkenborg
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Correspondence to Dirk Valkenborg.

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Zamanzad Ghavidel, F., Claesen, J., Burzykowski, T. et al. Comparison of the Mahalanobis Distance and Pearson’s χ2 Statistic as Measures of Similarity of Isotope Patterns. J. Am. Soc. Mass Spectrom. 25, 293–296 (2014). https://doi.org/10.1007/s13361-013-0773-z

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  • DOI: https://doi.org/10.1007/s13361-013-0773-z

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