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.
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
Link to chapter: https://link.springer.com/protocol/10.1007/978-1-0716-2445-6_18