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Analysis of Proteomic Data for Toxicological Applications

  • Protocol
Computational Systems Toxicology

Abstract

Toward a comprehensive characterization of toxicant responses, systems toxicology requires the integration of different data modalities. Proteomics approaches measure changes in the levels of proteins and their posttranslational modifications, which can closely reflect the biological effects of a toxicant. With a focus on mass spectrometry-based proteomics, we describe the isobaric tag-based approach for quantitative proteomics (iTRAQ® and TMT) and describe computational approaches to derive biological/mechanistic insights. Specifically, we describe the generation and quantification of mass-spectrometry data and the identification of affected proteins, functional modules, and protein subnetworks. We illustrate these approaches using results from a 90-day rat inhalation toxicology study. Overall, we provide the foundation to employ quantitative proteomics within systems toxicology assessment strategies.

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Acknowledgment

The research described in this chapter of the book was funded by Philip Morris International.

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Titz, B. et al. (2015). Analysis of Proteomic Data for Toxicological Applications. In: Hoeng, J., Peitsch, M. (eds) Computational Systems Toxicology. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2778-4_11

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  • DOI: https://doi.org/10.1007/978-1-4939-2778-4_11

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2777-7

  • Online ISBN: 978-1-4939-2778-4

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