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Peptide-to-Protein Summarization: An Important Step for Accurate Quantification in Label-Based Proteomics

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Mass Spectrometry of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1977))

Abstract

Quantitative MS/MS-based measurements are assessed at the peptide spectrum level and substantial variance is frequently observed for any given protein. Protein quantification requires a peptide-to-protein summarization step. This important step has been little investigated and most strategies only rely on quantitative spectrum values, ignoring a wealth of additional feature information is available for peptide spectra.

In this chapter, we discuss summarization methods that can be applied for label-based protein quantification. In particular, we focus on strategies using peptide spectrum characteristics in addition to quantitative values for protein abundance inference. We highlight significant relations of spectrum features and quantification accuracy to assess the reliability of spectra and the development of a correction. As a result, spectra of lower quality are identified, their impact is minimized and overall protein quantification is improved. Here, we investigate different peptide features in detail, emphasize the benefits of integrating spectrum feature information, and provide recommendations on the usage of the methods.

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Author information

Authors and Affiliations

  1. Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany

    Martina Fischer, Thilo Muth & Bernhard Y. Renard

Authors
  1. Martina Fischer
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  2. Thilo Muth
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  3. Bernhard Y. Renard
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Corresponding author

Correspondence to Bernhard Y. Renard .

Editor information

Editors and Affiliations

  1. Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, South Yorkshire, UK

    Caroline A. Evans

  2. Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne, UK

    Phillip C. Wright

  3. Laboratoire GBCM (EA4627), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France

    Josselin Noirel

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Fischer, M., Muth, T., Renard, B.Y. (2019). Peptide-to-Protein Summarization: An Important Step for Accurate Quantification in Label-Based Proteomics. In: Evans, C., Wright, P., Noirel, J. (eds) Mass Spectrometry of Proteins. Methods in Molecular Biology, vol 1977. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9232-4_11

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  • DOI: https://doi.org/10.1007/978-1-4939-9232-4_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9231-7

  • Online ISBN: 978-1-4939-9232-4

  • eBook Packages: Springer Protocols

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