Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for 
Circadian Analysis

Brüning, Franziska; Humphrey, Sean J.; Robles, Maria S.

doi:10.1007/978-1-0716-0381-9_14

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Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for Circadian Analysis

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Brüning, Franziska
Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society;

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Citation

Brüning, F., Humphrey, S. J., & Robles, M. S. (2021). Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for Circadian Analysis. In S. A. Brown (Ed.), Circadian Clocks. Methods in Molecular Biology, vol 2130. (pp. 185-193). New York, NY: Humana.

Cite as: https://hdl.handle.net/21.11116/0000-0009-7B7E-1

Abstract

Recent advances in mass spectrometry (MS)-based quantitative proteomics now allow the identification and quantification of deep proteomes and post-translational modifications (PTMs) in relatively short times. Therefore, in the last few years, this technology has proven successful in the circadian field to characterize temporal oscillations of the proteome and more recently PTMs in cellular systems and in tissues. In this chapter, we describe a robust and simple protocol, based on the EasyPhos workflow, to enable preparation of large number of proteomes and phosphoproteomes from mouse tissues for MS-based quantitative analysis. We additionally discuss computational methods to analyze proteome and phosphoproteome time series to determine circadian oscillations.