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Proteomic Sample Preparation and Data Analysis in Line with the Archaeal Proteome Project

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Archaea

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2522))

Abstract

Despite the ecological, evolutionary and economical significance of archaea, key aspects of their cell biology, metabolic pathways, and adaptations to a wide spectrum of environmental conditions, remain to be elucidated. Proteomics allows for the system-wide analysis of proteins, their changes in abundance between different conditions, as well as their post-translational modifications, providing detailed insights into the function of proteins and archaeal cell biology. In this chapter, we describe a sample preparation and mass spectrometric analysis workflow that has been designed for Haloferax volcanii but can be applied to a broad range of archaeal species. Furthermore, proteomics experiments provide a wealth of data that is invaluable to various disciplines. Therefore, we previously initiated the Archaeal Proteome Project (ArcPP), a community project that combines the analysis of multiple datasets with expert knowledge in various fields of archaeal research. The corresponding bioinformatic analysis, allowing for the integration of new proteomics data into the ArcPP, as well as the interactive exploration of ArcPP results is also presented here. In combination, these protocols facilitate an optimized, detailed and collaborative approach to archaeal proteomics.

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Acknowledgments

Continuous support and contributions to ArcPP by all ArcPP collaborators are greatly acknowledged. This work was supported by the National Science Foundation Grant 1817518.

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Authors and Affiliations

  1. Department of Biology, University of Pennsylvania, Philadelphia, PA, USA

    Stefan Schulze & Mechthild Pohlschroder

Authors
  1. Stefan Schulze
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  2. Mechthild Pohlschroder
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Corresponding authors

Correspondence to Stefan Schulze or Mechthild Pohlschroder .

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Editors and Affiliations

  1. Cellular Biochemistry of Microorganisms - Biochemie III, Universität Regensburg, Regensburg, Bayern, Germany

    Sébastien Ferreira-Cerca

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Schulze, S., Pohlschroder, M. (2022). Proteomic Sample Preparation and Data Analysis in Line with the Archaeal Proteome Project. In: Ferreira-Cerca, S. (eds) Archaea. Methods in Molecular Biology, vol 2522. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2445-6_18

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  • DOI: https://doi.org/10.1007/978-1-0716-2445-6_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2444-9

  • Online ISBN: 978-1-0716-2445-6

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