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An experimental design to extract more information from MS-based histone studies

Laura De Clerck (UGent) , Sander Willems, Simon Daled (UGent) , Bart Van Puyvelde (UGent) , Sigrid Verhelst (UGent) , Laura Corveleyn (UGent) , Dieter Deforce (UGent) and Maarten Dhaenens (UGent)
(2021) MOLECULAR OMICS. 17(6). p.929-938
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Abstract
Histone-based chromatin organization paved the way for eukaryotic genome complexity. Because of their key role in information management, the histone posttranslational modifications (hPTM), which mediate their function, have evolved into an alphabet that has more letters than there are amino acids, together making up the ‘‘histone code’’. The resulting combinatorial complexity is manifold higher than what is usually encountered in proteomics. Consequently, a considerably bigger part of the acquired MSMS spectra remains unannotated to date. Adapted search parameters can dig deeper into the dark histone ion space, but the lack of false discovery rate (FDR) control and the high level of ambiguity when searching combinatorial PTMs makes it very hard to assess whether the newly assigned ions are informative. Therefore, we propose an easily adoptable time-lapse enzymatic deacetylation (HDAC1) of a commercial histone extract as a quantify-first strategy that allows isolating ion populations of interest, when studying e.g. acetylation on histones, that currently remain in the dark. By adapting search parameters to study potential issues in sample preparation, data acquisition and data analysis, we stepwise managed to double the portion of annotated precursors of interest from 10.5% to 21.6%. This strategy is intended to make up for the lack of validated FDR control and has led to several adaptations of our current workflow that will reduce the portion of the dark histone ion space in the future. Finally, this strategy can be applied with any enzyme targeting a modification of interest
Keywords
Genetics, Molecular Biology, Biochemistry

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MLA
De Clerck, Laura, et al. “An Experimental Design to Extract More Information from MS-Based Histone Studies.” MOLECULAR OMICS, vol. 17, no. 6, 2021, pp. 929–38, doi:10.1039/d1mo00201e.
APA
De Clerck, L., Willems, S., Daled, S., Van Puyvelde, B., Verhelst, S., Corveleyn, L., … Dhaenens, M. (2021). An experimental design to extract more information from MS-based histone studies. MOLECULAR OMICS, 17(6), 929–938. https://doi.org/10.1039/d1mo00201e
Chicago author-date
De Clerck, Laura, Sander Willems, Simon Daled, Bart Van Puyvelde, Sigrid Verhelst, Laura Corveleyn, Dieter Deforce, and Maarten Dhaenens. 2021. “An Experimental Design to Extract More Information from MS-Based Histone Studies.” MOLECULAR OMICS 17 (6): 929–38. https://doi.org/10.1039/d1mo00201e.
Chicago author-date (all authors)
De Clerck, Laura, Sander Willems, Simon Daled, Bart Van Puyvelde, Sigrid Verhelst, Laura Corveleyn, Dieter Deforce, and Maarten Dhaenens. 2021. “An Experimental Design to Extract More Information from MS-Based Histone Studies.” MOLECULAR OMICS 17 (6): 929–938. doi:10.1039/d1mo00201e.
Vancouver
1.
De Clerck L, Willems S, Daled S, Van Puyvelde B, Verhelst S, Corveleyn L, et al. An experimental design to extract more information from MS-based histone studies. MOLECULAR OMICS. 2021;17(6):929–38.
IEEE
[1]
L. De Clerck et al., “An experimental design to extract more information from MS-based histone studies,” MOLECULAR OMICS, vol. 17, no. 6, pp. 929–938, 2021.
@article{8724229,
  abstract     = {{Histone-based chromatin organization paved the way for eukaryotic genome complexity. Because of
their key role in information management, the histone posttranslational modifications (hPTM), which
mediate their function, have evolved into an alphabet that has more letters than there are amino acids,
together making up the ‘‘histone code’’. The resulting combinatorial complexity is manifold higher than
what is usually encountered in proteomics. Consequently, a considerably bigger part of the acquired
MSMS spectra remains unannotated to date. Adapted search parameters can dig deeper into the dark
histone ion space, but the lack of false discovery rate (FDR) control and the high level of ambiguity
when searching combinatorial PTMs makes it very hard to assess whether the newly assigned ions are
informative. Therefore, we propose an easily adoptable time-lapse enzymatic deacetylation (HDAC1) of a
commercial histone extract as a quantify-first strategy that allows isolating ion populations of interest,
when studying e.g. acetylation on histones, that currently remain in the dark. By adapting search
parameters to study potential issues in sample preparation, data acquisition and data analysis, we
stepwise managed to double the portion of annotated precursors of interest from 10.5% to 21.6%. This
strategy is intended to make up for the lack of validated FDR control and has led to several adaptations
of our current workflow that will reduce the portion of the dark histone ion space in the future. Finally,
this strategy can be applied with any enzyme targeting a modification of interest}},
  author       = {{De Clerck, Laura and Willems, Sander and Daled, Simon and Van Puyvelde, Bart and Verhelst, Sigrid and Corveleyn, Laura and Deforce, Dieter and Dhaenens, Maarten}},
  issn         = {{2515-4184}},
  journal      = {{MOLECULAR OMICS}},
  keywords     = {{Genetics,Molecular Biology,Biochemistry}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{929--938}},
  title        = {{An experimental design to extract more information from MS-based histone studies}},
  url          = {{http://doi.org/10.1039/d1mo00201e}},
  volume       = {{17}},
  year         = {{2021}},
}

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