Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones

Simone Sidoli, Veit Schwämmle, Chrystian Ruminowicz, Thomas A. Hansen, Xudong Wu, Kristian Helin, Ole N. Jensen

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

We present an integrated middle-down proteomics platform for sensitive mapping and quantification of coexisting PTMs in large polypeptides (5-7 kDa).We combined an RP trap column with subsequent weak cation exchange-hydrophilic interaction LC interfaced directly to high mass accuracy ESI MS/MS using electron transfer dissociation. This enabled automated and efficient separation and sequencing of hypermodified histone N-terminal tails for unambiguous localization of combinatorial PTMs. We present Histone Coder and IsoScale software to extract, filter, and analyze MS/MS data, including quantification of cofragmenting isobaric polypeptide species. We characterized histone tails derived from murine embryonic stem cells knockout in suppressor of zeste12 (Suz12-/-) and quantified 256 combinatorial histone marks in histones H3, H4, and H2A. Furthermore, a total of 713 different combinatorial histone marks were identified in purified histone H3.Wemeasured a seven-fold reduction ofH3K27me2/me3 (where me2 and me3 are dimethylation and trimethylation, respectively) in Suz12-/- cells and detected significant changes of the relative abundance of 16 other single PTMs of histone H3 and other combinatorial marks. We conclude that the inactivation of Suz12 is associated with changes in the abundance of not only H3K27 methylation but also multiple other PTMs in histone H3 tails.

Original languageEnglish (US)
Pages (from-to)2200-2211
Number of pages12
JournalProteomics
Volume14
Issue number19
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

Fingerprint

Workflow
Post Translational Protein Processing
Tandem Mass Spectrometry
Chromatography
Histones
Mass spectrometry
Pulse time modulation
Histone Code
Peptides
Methylation
Embryonic Stem Cells
Hydrophobic and Hydrophilic Interactions
Exchange interactions
Proteomics
Stem cells
Cations
Software
Electrons

Keywords

  • Histones
  • Hybrid chromatography
  • Middle-down proteomics
  • Post-translational modifications
  • Stem cells
  • Technology

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. / Sidoli, Simone; Schwämmle, Veit; Ruminowicz, Chrystian; Hansen, Thomas A.; Wu, Xudong; Helin, Kristian; Jensen, Ole N.

In: Proteomics, Vol. 14, No. 19, 01.01.2014, p. 2200-2211.

Research output: Contribution to journalArticle

Sidoli, Simone ; Schwämmle, Veit ; Ruminowicz, Chrystian ; Hansen, Thomas A. ; Wu, Xudong ; Helin, Kristian ; Jensen, Ole N. / Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. In: Proteomics. 2014 ; Vol. 14, No. 19. pp. 2200-2211.
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