Phosphoproteome and Proteome Sample Preparation from Mouse Tissues for Circadian Analysis

Area of Science:

• Biochemistry
• Chronobiology
• Proteomics

Background:

• Mass spectrometry (MS)-based quantitative proteomics enables deep proteome and post-translational modification (PTM) analysis.
• This technology has been successfully applied to the circadian field for temporal proteome and PTM oscillation characterization.

Purpose of the Study:

• To describe a robust and simple protocol for preparing large numbers of mouse tissue proteomes and phosphoproteomes.
• To enable MS-based quantitative analysis of circadian oscillations in tissues.

Main Methods:

• Utilized the EasyPhos workflow for sample preparation.
• Applied MS-based quantitative proteomic and phosphoproteomic analysis.
• Employed computational methods for time-series data analysis.

Main Results:

• Successfully prepared proteomes and phosphoproteomes from mouse tissues.
• Enabled quantitative analysis of temporal oscillations.
• Facilitated the determination of circadian rhythms in protein and PTM levels.

Conclusions:

• The described protocol is effective for large-scale proteome and phosphoproteome analysis from mouse tissues.
• This workflow supports the investigation of circadian biology using quantitative MS.
• The methods allow for the identification and quantification of temporal protein dynamics and PTMs.