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Processing of Mass Spectrometry Data in Clinical Applications

  • Dario Di Silvestre
  • Pietro Brunetti
  • Pier Luigi Mauri
Chapter
Part of the Translational Bioinformatics book series (TRBIO, volume 3)

Abstract

Mass spectrometry-based proteomics has become the leading approach for analyzing complex biological samples at a large-scale level. Its importance for clinical applications is more and more increasing, thanks to the development of high-performing instruments which allow the discovery of disease-specific biomarkers and an automated and rapid protein profiling of the analyzed samples. In this scenario, the large-scale production of proteomic data has driven the development of specific bioinformatic tools to assist researchers during the discovery processes. Here, we discuss the main methods, algorithms, and procedures to identify and use biomarkers for clinical and research purposes. In particular, we have been focused on quantitative approaches, the identification of proteotypic peptides, and the classification of samples, using proteomic data. Finally, this chapter is concluded by reporting the integration of experimental data with network datasets, as valuable instrument for identifying alterations that underline the emergence of specific phenotypes. Based on our experience, we show some examples taking into consideration experimental data obtained by multidimensional protein identification technology (MudPIT) approach.

Keywords

Mass spectrometry-based proteomics Disease-specific biomarkers Bioinformatic tools Algorithms Integration Multidimensional protein identification technology 

Notes

Acknowledgments

This study was supported by the Italian Ministry of Economy and Finance to the CNR for the Project “FaReBio di Qualita,” by Italian Ministry of University and Research for the Project FAR and by Fondazione Cariplo (2010-0653).

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Dario Di Silvestre
    • 1
  • Pietro Brunetti
    • 1
  • Pier Luigi Mauri
    • 1
  1. 1.Proteomics and Metabolomics LaboratoryInstitute for Biomedical Technologies – National Research CouncilSegrate, MilanItaly

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