MassIVE MSV000097997

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In-cell proteomics enables high-resolution temporal profiling of cell cycle progression and DNA damage response in Saccharomyces cerevisiae

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Description

Yeast is a widely used model organism in biological and proteomics research. Conventional bottom-up proteomic analysis of yeast cells requires disruption of the rigid cell wall to extract proteins, which is often associated with lengthy procedures, significant technical variations and noticeable sample loss. Here, we present an “in-cell proteomics” approach that eliminates cell lysis and digests proteins directly in the yeast cells after a rapid methanol fixation. The approach integrates all the sample processing into a single filter device, offering a simple yet highly effective and sensitive approach for yeast proteomics analysis. We applied this approach to characterize proteome dynamics in the budding yeast Saccharomyces cerevisiae during cell cycle progression and following DNA damage. With single-shot LC-MS, we were able to detect and quantify around 3,500 yeast proteins from the in-cell digests. Our study presents a quantitative proteome map of yeast cell-cycle progression with high temporal resolution for cell division cycle (Cdc) proteins and introduces a novel in-cell proteomics approach for yeast. It also provides a comprehensive, time-resolved view of proteome-wide dynamics and remodeling throughout the yeast cell cycle and in response to methyl methanesulfonate (MMS)-induced DNA damage. [doi:10.25345/C50R9MG9K] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Quantitative proteomics ; In-cell proteomics ; On-filter in-cell (OFIC) digestion ; DNA damage ; DNA repair ; Yeast ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Zhihao Zhuang, Dept. of Chemistry & Biochemistry, University of Delaware, USA
Submitting User: yayu

Publications

Nwaora H, Yu Y, Zhuang Z.
In-Cell Proteomics Enables High-Resolution Temporal Profiling of Cell Cycle Progression and DNA Damage Response in Saccharomyces cerevisiae.
Proteomics. Epub 2025 Dec 18.

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