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Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions

Simon Daled (UGent) , Sander Willems, Bart Van Puyvelde (UGent) , Laura Corveleyn (UGent) , Sigrid Verhelst (UGent) , Laura De Clerck (UGent) , Dieter Deforce (UGent) and Maarten Dhaenens (UGent)
(2021) PROTEOMES. 9(2).
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Abstract
Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment between runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX(R), Genovis, Lund, Sweden), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues. Raw data are available via ProteomeXchange with identifier PXD024423.
Keywords
MIDDLE-DOWN PROTEOMICS, QUANTITATIVE ASSESSMENT, CYSTEINE PROTEINASE, SIDE REACTIONS, PROPIONYLATION, PERFORMANCE, DERIVATIZATION, PURIFICATION, GINGIPAIN, CODE, histone code, coverage, epigenetics, mass spectrometry, sample, preparation, workflow optimization, GingisREX

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MLA
Daled, Simon, et al. “Histone Sample Preparation for Bottom-up Mass Spectrometry : A Roadmap to Informed Decisions.” PROTEOMES, vol. 9, no. 2, 2021, doi:10.3390/proteomes9020017.
APA
Daled, S., Willems, S., Van Puyvelde, B., Corveleyn, L., Verhelst, S., De Clerck, L., … Dhaenens, M. (2021). Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions. PROTEOMES, 9(2). https://doi.org/10.3390/proteomes9020017
Chicago author-date
Daled, Simon, Sander Willems, Bart Van Puyvelde, Laura Corveleyn, Sigrid Verhelst, Laura De Clerck, Dieter Deforce, and Maarten Dhaenens. 2021. “Histone Sample Preparation for Bottom-up Mass Spectrometry : A Roadmap to Informed Decisions.” PROTEOMES 9 (2). https://doi.org/10.3390/proteomes9020017.
Chicago author-date (all authors)
Daled, Simon, Sander Willems, Bart Van Puyvelde, Laura Corveleyn, Sigrid Verhelst, Laura De Clerck, Dieter Deforce, and Maarten Dhaenens. 2021. “Histone Sample Preparation for Bottom-up Mass Spectrometry : A Roadmap to Informed Decisions.” PROTEOMES 9 (2). doi:10.3390/proteomes9020017.
Vancouver
1.
Daled S, Willems S, Van Puyvelde B, Corveleyn L, Verhelst S, De Clerck L, et al. Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions. PROTEOMES. 2021;9(2).
IEEE
[1]
S. Daled et al., “Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions,” PROTEOMES, vol. 9, no. 2, 2021.
@article{8718180,
  abstract     = {{Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment between runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX(R), Genovis, Lund, Sweden), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues. Raw data are available via ProteomeXchange with identifier PXD024423.}},
  articleno    = {{17}},
  author       = {{Daled, Simon and Willems, Sander and Van Puyvelde, Bart and Corveleyn, Laura and Verhelst, Sigrid and De Clerck, Laura and Deforce, Dieter and Dhaenens, Maarten}},
  issn         = {{2227-7382}},
  journal      = {{PROTEOMES}},
  keywords     = {{MIDDLE-DOWN PROTEOMICS,QUANTITATIVE ASSESSMENT,CYSTEINE PROTEINASE,SIDE REACTIONS,PROPIONYLATION,PERFORMANCE,DERIVATIZATION,PURIFICATION,GINGIPAIN,CODE,histone code,coverage,epigenetics,mass spectrometry,sample,preparation,workflow optimization,GingisREX}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{18}},
  title        = {{Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions}},
  url          = {{http://doi.org/10.3390/proteomes9020017}},
  volume       = {{9}},
  year         = {{2021}},
}
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