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Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies

Author

Listed:
  • Kakourou Alexia
  • Mertens Bart

    (Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands)

  • Vach Werner

    (Center for Medical Biometry and Medical Informatics, University of Freiburg, Freiburg, Germany)

  • Nicolardi Simone
  • van der Burgt Yuri

    (Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands)

Abstract

Mass spectrometry based clinical proteomics has emerged as a powerful tool for high-throughput protein profiling and biomarker discovery. Recent improvements in mass spectrometry technology have boosted the potential of proteomic studies in biomedical research. However, the complexity of the proteomic expression introduces new statistical challenges in summarizing and analyzing the acquired data. Statistical methods for optimally processing proteomic data are currently a growing field of research. In this paper we present simple, yet appropriate methods to preprocess, summarize and analyze high-throughput MALDI-FTICR mass spectrometry data, collected in a case-control fashion, while dealing with the statistical challenges that accompany such data. The known statistical properties of the isotopic distribution of the peptide molecules are used to preprocess the spectra and translate the proteomic expression into a condensed data set. Information on either the intensity level or the shape of the identified isotopic clusters is used to derive summary measures on which diagnostic rules for disease status allocation will be based. Results indicate that both the shape of the identified isotopic clusters and the overall intensity level carry information on the class outcome and can be used to predict the presence or absence of the disease.

Suggested Citation

  • Kakourou Alexia & Mertens Bart & Vach Werner & Nicolardi Simone & van der Burgt Yuri, 2016. "Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(5), pages 415-430, October.
    • Handle: RePEc:bpj:sagmbi:v:15:y:2016:i:5:p:415-430:n:4
    DOI: 10.1515/sagmb-2016-0005
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    References listed on IDEAS

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    1. S. le Cessie & J. C. van Houwelingen, 1992. "Ridge Estimators in Logistic Regression," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 41(1), pages 191-201, March.
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