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Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions

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 mod...

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Autores principales: Daled, Simon, Willems, Sander, Van Puyvelde, Bart, Corveleyn, Laura, Verhelst, Sigrid, De Clerck, Laura, Deforce, Dieter, Dhaenens, Maarten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167631/
https://www.ncbi.nlm.nih.gov/pubmed/33919160
http://dx.doi.org/10.3390/proteomes9020017
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author Daled, Simon
Willems, Sander
Van Puyvelde, Bart
Corveleyn, Laura
Verhelst, Sigrid
De Clerck, Laura
Deforce, Dieter
Dhaenens, Maarten
author_facet Daled, Simon
Willems, Sander
Van Puyvelde, Bart
Corveleyn, Laura
Verhelst, Sigrid
De Clerck, Laura
Deforce, Dieter
Dhaenens, Maarten
author_sort Daled, Simon
collection PubMed
description 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(®), 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.
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spelling pubmed-81676312021-06-02 Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions Daled, Simon Willems, Sander Van Puyvelde, Bart Corveleyn, Laura Verhelst, Sigrid De Clerck, Laura Deforce, Dieter Dhaenens, Maarten Proteomes Article 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(®), 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. MDPI 2021-04-21 /pmc/articles/PMC8167631/ /pubmed/33919160 http://dx.doi.org/10.3390/proteomes9020017 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Daled, Simon
Willems, Sander
Van Puyvelde, Bart
Corveleyn, Laura
Verhelst, Sigrid
De Clerck, Laura
Deforce, Dieter
Dhaenens, Maarten
Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
title Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
title_full Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
title_fullStr Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
title_full_unstemmed Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
title_short Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions
title_sort histone sample preparation for bottom-up mass spectrometry: a roadmap to informed decisions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167631/
https://www.ncbi.nlm.nih.gov/pubmed/33919160
http://dx.doi.org/10.3390/proteomes9020017
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