Sucrose gradient chromatin enrichment for quantitative proteomics analysis in budding yeast

STAR Protoc. 2021 Sep 14;2(4):100825. doi: 10.1016/j.xpro.2021.100825. eCollection 2021 Dec 17.

Abstract

Here, we describe a fractionation protocol optimized to quantify changes in relative abundance of the chromatin-bound proteome (chromatome) by tandem mass tag multiplexing-based tandem mass spectrometry. It has been applied to yeast cells before and after exposure to DNA-damaging drugs to characterize changes in chromatin composition induced by the DNA damage response. We detail steps for stringent chromatin fractionation, sample preparation for mass spectrometry, and its evaluation. For complete details on the use and execution of this protocol, please refer to Challa et al. (2021).

Keywords: Bioinformatics; Cell Biology; Cell separation/fractionation; Mass Spectrometry; Model Organisms; Protein Biochemistry; Proteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin* / chemistry
  • Chromatin* / genetics
  • Chromatin* / isolation & purification
  • Proteome* / analysis
  • Proteome* / chemistry
  • Proteome* / genetics
  • Proteomics / methods*
  • Saccharomycetales* / chemistry
  • Saccharomycetales* / genetics
  • Saccharomycetales* / metabolism
  • Sucrose / chemistry*
  • Tandem Mass Spectrometry / methods

Substances

  • Chromatin
  • Proteome
  • Sucrose