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Analysis of Labeled Quantitative Mass Spectrometry Proteomics Data

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Abstract

Proteomics has an important role in biomedical research. Using mass spectrometry (MS), researchers are able to identify proteins on a large scale. Mass spectrometers measure mass spectra of peptides on the basis of which software packages can infer protein detection. By tagging proteins from distinct samples with heavy and light mass labels, relative protein abundances in different conditions are compared, e.g., healthy versus diseased individuals. The quantification of proteins in complex samples, the monitoring of specific post-translational modification (PTM) changes, and the identification of biomarkers pose challenges to the experimentalists and to the algorithmic and statistical techniques applied.

This chapter gives an overview of the methods used to label proteins and to follow their changes in abundance in biomedical samples, and of the bioinformatics methods related to isotopic and isobaric labeling. Tools to process the data and to perform downstream analyses are presented as well.

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Notes

  1. 1.

    Mass spectrometers are capable of separating and detecting individual ions—even those that only differ by a single atomic mass unit. As a result molecules containing different isotopes can be distinguished. Natural isotopes occur with well-known abundances and depend on molecular formula of peptide.

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  1. Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria

    Jacques Colinge

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  1. Florian Paul Breitwieser
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  2. Jacques Colinge
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Correspondence to Jacques Colinge .

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  1. , Section for Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria

    Zlatko Trajanoski

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Breitwieser, F.P., Colinge, J. (2012). Analysis of Labeled Quantitative Mass Spectrometry Proteomics Data. In: Trajanoski, Z. (eds) Computational Medicine. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0947-2_5

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