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The Proteomics Toolbox Applied to Peroxisomes

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Molecular Machines Involved in Peroxisome Biogenesis and Maintenance

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Abstract

The full understanding of a cell’s functionality and activity requires comprehensive knowledge about the properties and the individual contribution of all players involved, both as single entities and as parts of functional units such as membrane-enclosed organelles or larger multi-protein complexes. This comprises, among others, the gathering of information about the accurate subcellular localization of proteins and the interaction networks they form as well as dynamic alterations thereof upon metabolic, developmental, or environmental changes. The proteomics toolbox provides us here with a powerful means for the systematic, discovery-driven analysis of protein properties on a proteome-wide scale. In clever combination with classical biochemical or cell biological methods, state-of-the-art mass spectrometry (MS)-based proteomics has boosted the functional and quantitative analysis of proteins beyond the sheer generation of identification lists.

In this chapter, we will highlight the potential of modern MS-based proteomics research for the in-depth analysis of different aspects of peroxisome biology. The focus will be on quantitative MS strategies based on label-free (e.g., protein correlation profiling) or stable isotope-labeling techniques. We will review the applicability of these powerful approaches to the virtually complete delineation of the peroxisomal proteome including the discovery of new peroxisomal constituents as well as the characterization of peroxisomal membrane protein complexes providing new insights into distinct aspects of biogenesis and functioning of peroxisomes.

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Abbreviations

AP:

Affinity purification

AP-AM:

Affinity purification after mixing

AP-MS:

Affinity purification-mass spectrometry

AP-PM:

Affinity purification prior to mixing

ER:

Endoplasmic reticulum

ESI:

Electrospray ionization

GFP:

Green fluorescence protein

GPF:

Gas phase fractionation

ICAT:

Isotope-coded affinity tag

iTRAQ:

Isobaric tags for absolute and relative quantification

LC:

Liquid chromatography

MALDI:

Matrix-assisted laser desorption/ionization

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

PA:

Protein A

POI:

Protein of interest

PPI:

Protein–protein interactions

PTM:

Posttranslational modification

PTS:

Peroxisomal targeting signal

QTOF:

Quadrupole time of flight

SILAC:

Stable isotope labeling with amino acids in cell culture

TAP:

Tandem affinity purification

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Acknowledgments

We would like to apologize to all the scientists whose work was not cited. This work was supported by grants of the Deutsche Forschungsgemeinschaft (FOR1905) and the Excellence Initiative of the German Federal & State Governments (Grant EXC 294 BIOSS Centre for Biological Signalling Studies).

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Authors and Affiliations

  1. Institute of Biology II and BIOSS—Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany

    Silke Oeljeklaus, Andreas Schummer & Bettina Warscheid

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  1. Silke Oeljeklaus
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  2. Andreas Schummer
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Correspondence to Bettina Warscheid .

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  1. Mauerbach, Austria

    Cecile Brocard

  2. Max F. Perutz Laboratories University of Vienna, Vienna, Austria

    Andreas Hartig

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Oeljeklaus, S., Schummer, A., Warscheid, B. (2014). The Proteomics Toolbox Applied to Peroxisomes. In: Brocard, C., Hartig, A. (eds) Molecular Machines Involved in Peroxisome Biogenesis and Maintenance. Springer, Vienna. https://doi.org/10.1007/978-3-7091-1788-0_12

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