Mass Spectrometry and Epigenetics

  • Luciano Nicosia
  • Roberta Noberini
  • Monica Soldi
  • Alessandro Cuomo
  • Daniele Musiani
  • Valeria Spadotto
  • Tiziana BonaldiEmail author
Reference work entry


Chromatin is a nucleoprotein complex composed of DNA and histone proteins. The concerted activity of chromatin-associated proteins, histone post-translational modifications, and DNA methylation induces epigenetic variations that regulate most of the physiological processes of eukaryotic cells, ranging from gene expression to DNA replication and repair. Epigenetics has also been shown to be tightly linked to cell metabolism. For instance, histone modifications are highly sensitive to the changes in the microenvironment and the local concentration of specific metabolites. Mass-spectrometry (MS)-based proteomics significantly contributed to the recent advances in the epigenetic field, by allowing the comprehensive analysis of histone post-translational modifications as well as the systematic identification of chromatin constituents.

In this chapter, we will provide a general overview of various MS-based experimental strategies developed to boost the epigenetic field, with references to the studies whereby chromatin biology was assessed in relation to cell metabolism.


Mass spectrometry Histone post-translational modifications Chromatin Metabolism Epigenetics Stable isotope labeling with amino acids in cell culture Chromatin-associated proteins Histone modifying enzymes Proteomics Global post-translational modification profiling 

List of Abbreviations


Antisecretor factor 10


Chromatin immunoprecipitation


Collision-induced dissociation


Clustered regularly interspaced short palindromic repeats


Data-dependent acquisition


Electron capture dissociation


Embryonic stem cell


Electron transfer dissociation


Histone acetyltransferase




Heavy-methyl SILAC


Lysine acetyl-transferase


Liquid chromatography




Multiple reaction monitoring




Neural progenitor cell


Neural stem cell


Post-translational modification


Relative abundance






Stable isotope labeling with amino acids in cell culture


Selected reaction monitoring


Transcription activator-like


Transcription factor


Weak-cation exchange hydrophilic interaction liquid chromatography


MS-extracted ion chromatogram


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Luciano Nicosia
    • 1
  • Roberta Noberini
    • 2
  • Monica Soldi
    • 1
  • Alessandro Cuomo
    • 1
  • Daniele Musiani
    • 1
  • Valeria Spadotto
    • 1
  • Tiziana Bonaldi
    • 1
    Email author
  1. 1.Department of Experimental OncologyEuropean Institute of OncologyMilanItaly
  2. 2.Center for Genomic Science of IIT@SEMMIstituto Italiano di TecnologiaMilanItaly

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