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

  • Fatemeh Zamanzad Ghavidel
  • Jürgen Claesen
  • Tomasz Burzykowski
  • Dirk Valkenborg
Application Note


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.

Key words

Similarity statistics Isotope distributions Mass spectral data interpretation Bioinformatics  Mahalanobis distance 



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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Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  • Fatemeh Zamanzad Ghavidel
    • 1
  • Jürgen Claesen
    • 1
  • Tomasz Burzykowski
    • 1
  • Dirk Valkenborg
    • 1
    • 2
    • 3
  1. 1.I-BioStatHasselt UniversityHasseltBelgium
  2. 2.Applied Bio and Molecular SystemsFlemish Institute for Technological Research, VITOMolBelgium
  3. 3.Center for ProteomicsAntwerpBelgium

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