PXD009910

PXD009910 is an original dataset announced via ProteomeXchange.

Title	An experimental design to extract more information from MS-based histone studies
Description	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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:05:37.234.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD009910
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	acetylated residue; formylated residue; deamidated residue
Instrument	SYNAPT G2-Si

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-25 06:06:18	ID requested
1	2022-10-04 01:47:32	announced
⏵ 2	2023-11-14 08:05:40	announced	2023-11-14: Updated project metadata.

De Clerck L, Willems S, Daled S, Van Puyvelde B, Verhelst S, Corveleyn L, Deforce D, Dhaenens M, An experimental design to extract more information from MS-based histone studies. Mol Omics, 17(6):929-938(2021) [pubmed]

submitter keyword: histone post-translational modifications

LC-MS/MS

proteomics

identification

HDAC

Maarten Dhaenens
contact affiliation	Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical science, Ghent University, Belgium
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/10/PXD009910

PRIDE project URI

• PRIDE
  1. PXD009910
     1. Label: PRIDE project
     2. Name: An experimental design to extract more information from MS-based histone studies