A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes

Nat Commun. 2018 Jun 13;9(1):2311. doi: 10.1038/s41467-018-04619-5.


Understanding the dynamics of endogenous protein-protein interactions in complex networks is pivotal in deciphering disease mechanisms. To enable the in-depth analysis of protein interactions in chromatin-associated protein complexes, we have previously developed a method termed RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins). Here, we present a quantitative multiplexed method (qPLEX-RIME), which integrates RIME with isobaric labelling and tribrid mass spectrometry for the study of protein interactome dynamics in a quantitative fashion with increased sensitivity. Using the qPLEX-RIME method, we delineate the temporal changes of the Estrogen Receptor alpha (ERα) interactome in breast cancer cells treated with 4-hydroxytamoxifen. Furthermore, we identify endogenous ERα-associated proteins in human Patient-Derived Xenograft tumours and in primary human breast cancer clinical tissue. Our results demonstrate that the combination of RIME with isobaric labelling offers a powerful tool for the in-depth and quantitative characterisation of protein interactome dynamics, which is applicable to clinical samples.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breast Neoplasms / metabolism
  • Chromatin / chemistry
  • Chromatin / drug effects
  • Chromatin / metabolism*
  • Estrogen Receptor alpha / chemistry
  • Estrogen Receptor alpha / metabolism
  • Female
  • Heterografts
  • Humans
  • MCF-7 Cells
  • Mass Spectrometry / methods*
  • Mice
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps / drug effects
  • Selective Estrogen Receptor Modulators / pharmacology
  • Tamoxifen / analogs & derivatives
  • Tamoxifen / pharmacology


  • Chromatin
  • ESR1 protein, human
  • Estrogen Receptor alpha
  • Multiprotein Complexes
  • Selective Estrogen Receptor Modulators
  • Tamoxifen
  • afimoxifene