Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

  • Mowei Zhou
  • Si Wu
  • David L. Stenoien
  • Zhaorui Zhang
  • Lanelle Connolly
  • Michael Freitag
  • Ljiljana Paša-Tolić
Part of the Methods in Molecular Biology book series (MIMB, volume 1507)


Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Key words

Histone Post-translational modification Liquid chromatography Mass spectrometry Top-down Screening 



The authors thank Christopher Wilkins, Jung Kap Park, and Sangtae Kim at the Pacific Northwest National Laboratory (PNNL) for developing the bioinformatics software used in this work. We appreciate the help from other PNNL colleagues: Matthew Monroe and Nikola Tolić for data analysis and Rosalie K. Chu, Rui Zhao, Anil K. Shukla, and Ron Moore for running LCMS experiments. We also thank Jonathan Galazka at the Oregon State University for preparing the fungal histone samples. The research was performed in Environmental Molecular Sciences Laboratory (EMSL), a US Department of Energy (DOE) national user facility at the Pacific Northwest National Laboratory (PNNL) in Richland, WA.


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Mowei Zhou
    • 1
  • Si Wu
    • 1
    • 2
  • David L. Stenoien
    • 1
  • Zhaorui Zhang
    • 1
  • Lanelle Connolly
    • 3
  • Michael Freitag
    • 3
  • Ljiljana Paša-Tolić
    • 1
  1. 1.Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of OklahomaNormanUSA
  3. 3.Department of Biochemistry and Biophysics, Center for Genome Research and BiocomputingOregon State UniversityCorvallisUSA

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