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Absolute Protein Quantification Using AQUA-Calibrated 2D-PAGE

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Microbial Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1841))

Abstract

Absolute protein quantification for the analysis of proteome dynamics is more and more required by the scientific community. Therefore a number of methods have recently been reported that aim at determining concentrations of single proteins in complex samples, all of them having their advantages and limitations. However, for all of these methods an accurate and protein unspecific determination of the total protein amount in a given sample is urgently needed. Here a ninhydrin-based assay established to reach this goal is described. Moreover, an optimized protocol for protein digestion is an inevitable prerequisite for all mass spectrometry-based approaches aiming at absolute protein quantification. In this chapter, various aspects are described which have to be considered during validation of a suitable digestion method and a detailed protocol is presented that can be applied to the digestion of soluble proteins originated from microbes.

In order to provide an absolute protein quantification workflow applicable for small scale and large scale approaches, a step-by-step guide is provided for the so-called AQUA-strategy (AQUA = absolute quantification), including selection of suited standard peptides, the development of optimized MS methods and the determination of absolute protein concentration using stable isotope dilution and selected reaction monitoring (SID-SRM). Subsequently, a workflow is introduced that combines targeted mass spectrometry and two-dimensional polyacrylamide gel electrophoresis for the large-scale determination of absolute protein amounts.

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Acknowledgments

This work was supported by the German Research Foundation Grant SFB/TR34.

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Authors and Affiliations

  1. Department of Microbial Proteomics, Institute for Microbiology, University Greifswald, Greifswald, Germany

    Sandra Maaß

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  1. Sandra Maaß
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Correspondence to Sandra Maaß .

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Editors and Affiliations

  1. Department of Microbial Proteomics, Institute for Microbiology, University Greifswald, Greifswald, Germany

    Dörte Becher

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Maaß, S. (2018). Absolute Protein Quantification Using AQUA-Calibrated 2D-PAGE. In: Becher, D. (eds) Microbial Proteomics. Methods in Molecular Biology, vol 1841. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8695-8_11

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  • DOI: https://doi.org/10.1007/978-1-4939-8695-8_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8693-4

  • Online ISBN: 978-1-4939-8695-8

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