Abstract
Mass spectrometry-based quantitative proteomics have greatly benefited from recent technological and computational improvements, allowing quantification of proteomes at continually increasing depth. From a growing number of quantitative proteomic studies in the circadian field in the last years, it has become evident that protein cycles differ significantly from transcript rhythmicity and protein abundance cannot be generally extrapolated from transcriptomic investigations. As proteins are the functional entities of cellular processes, our understanding of rhythmic biology relies thus on the investigation of protein abundance and its post-translational modification state, as proxy of their activity. In this chapter, we present a robust and simple method to prepare and quantitatively measure proteomes and phosphoproteomes in a highly parallelizable manner. We further discuss key factors to be considered when designing time course experiments and during data analysis with the aim to accurately identify circadian and sleep-driven oscillations in proteome and phosphoproteome.
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Kliem, F.P., Brüning, F., Robles, M.S. (2022). Proteomics Approaches to Assess Sleep and Circadian Rhythms. In: Hirota, T., Hatori, M., Panda, S. (eds) Circadian Clocks. Neuromethods, vol 186. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2577-4_15
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DOI: https://doi.org/10.1007/978-1-0716-2577-4_15
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