Epiprofile quantifies histone peptides with modifications by extracting retention time and intensity in high-resolution mass spectra

Zuo Fei Yuan, Shu Lin, Rosalynn C. Molden, Xing Jun Cao, Natarajan V. Bhanu, Xiaoshi Wang, Simone Sidoli, Shichong Liu, Benjamin A. Garcia

Research output: Contribution to journalArticle

Abstract

Histone post-translational modifications contribute to chromatin function through their chemical properties which influence chromatin structure and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (nanoLC-MS/MS) has emerged as the most suitable technology for global histone modification analysis because of the high sensitivity and the high mass accuracy of this approach that provides confident identification. However, analysis of histones with this method is even more challenging because of the large number and variety of isobaric histone peptides and the high dynamic range of histone peptide abundances. Here, we introduce EpiProfile, a software tool that discriminates isobaric histone peptides using the distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. The accuracy of EpiProfile was evaluated by analysis of mixtures containing different ratios of synthetic histone peptides. In addition to labelfree quantification of histone peptides, EpiProfile is flexible and can quantify different types of isotopically labeled histone peptides. EpiProfile is unique in generating layouts (i.e. relative retention time) of histone peptides when compared with manual quantification of the data and other programs (such as Skyline), filling the need of an automatic and freely available tool to quantify labeled and non-labeled modified histone peptides. In summary, EpiProfile is a valuable nanoflow liquid chromatography coupled with high resolution tandem mass spectrometrybased quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples.

Original languageEnglish (US)
Pages (from-to)1696-1707
Number of pages12
JournalMolecular and Cellular Proteomics
Volume14
Issue number6
DOIs
StatePublished - Jun 1 2015
Externally publishedYes

Fingerprint

Tandem Mass Spectrometry
HeLa Cells
Liquid Chromatography
Histones
Peptides
Chromatin
Histone Code
Post Translational Protein Processing
Area Under Curve
Proteins
Software
Ions
Technology

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology

Cite this

Epiprofile quantifies histone peptides with modifications by extracting retention time and intensity in high-resolution mass spectra. / Yuan, Zuo Fei; Lin, Shu; Molden, Rosalynn C.; Cao, Xing Jun; Bhanu, Natarajan V.; Wang, Xiaoshi; Sidoli, Simone; Liu, Shichong; Garcia, Benjamin A.

In: Molecular and Cellular Proteomics, Vol. 14, No. 6, 01.06.2015, p. 1696-1707.

Research output: Contribution to journalArticle

Yuan, Zuo Fei ; Lin, Shu ; Molden, Rosalynn C. ; Cao, Xing Jun ; Bhanu, Natarajan V. ; Wang, Xiaoshi ; Sidoli, Simone ; Liu, Shichong ; Garcia, Benjamin A. / Epiprofile quantifies histone peptides with modifications by extracting retention time and intensity in high-resolution mass spectra. In: Molecular and Cellular Proteomics. 2015 ; Vol. 14, No. 6. pp. 1696-1707.
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