Dataset Information

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

ABSTRACT: The combinatorial complexity of histone samples 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 use 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.

INSTRUMENT(S): SYNAPT G2-Si

ORGANISM(S): Bos Taurus (bovine)

TISSUE(S): Thymus

SUBMITTER: Maarten Dhaenens

LAB HEAD: Maarten Dhaenens

PROVIDER: PXD009910 | Pride | 2022-10-04

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	180201_MD_HDAC_HDDDDA_0min_A.raw.zip	Raw
	180201_MD_HDAC_HDDDDA_0min_B.raw.zip	Raw
	180201_MD_HDAC_HDDDDA_0min_C.raw.zip	Raw
	180201_MD_HDAC_HDDDDA_0min_D.raw.zip	Raw
	180201_MD_HDAC_HDDDDA_0min_neg_A.raw.zip	Raw

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

De Clerck Laura L Willems Sander S Daled Simon S Van Puyvelde Bart B Verhelst Sigrid S Corveleyn Laura L Deforce Dieter D Dhaenens Maarten M

Molecular omics 20211206 6

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 acquire ...[more]

PMID: 34522942

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