PXD019652

PXD019652 is an original dataset announced via ProteomeXchange.

Title	Comprehensive Histone Epigenetics (CHEpi): A mass spectrometry based screening assay to measure epigenetic toxicity
Description	Epigenetics have taken center stage in the study of diseases such as cancer, diabetes, and neurodegeneration. For nearly thirty years, it has been known that cancer cells exhibit abnormal DNA methylation patterns. In contrast, the large scale analysis of histone posttranslational modifications (hPTMs) has lagged behind because classically, histone modification analysis has relied on site specific antibody-based techniques. Mass spectrometry (MS) is a technique that holds the promise to picture the histone code comprehensively in a single experiment. Therefore, we developed an MS-based method that is capable of tracking all possible hPTMs in an untargeted approach. In this way, trends in single and combinatorial hPTMs can be reported and enable prediction of the epigenetic toxicity of compounds. Moreover, this method is based on the use of human embryonic stem cells (hESCs), thereby omitting the need to sacrifice laboratory animals. Improving the workflow and the user-friendliness of the assay is an ongoing effort. Still, this novel toxicoepigenetic assay and the data it generates holds great potential for, among others, pharmaceutical industry, food science, clinical diagnostics and, environmental toxicity screening.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:13:14.879.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019652
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; formylated residue; monohydroxylated residue; acetylated residue; deamidated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-08 07:45:37	ID requested
1	2020-10-12 06:54:21	announced
⏵ 2	2024-10-22 05:13:15	announced	2024-10-22: Updated project metadata.

Verhelst S, De Clerck L, Willems S, Van Puyvelde B, Daled S, Deforce D, Dhaenens M, Comprehensive histone epigenetics: A mass spectrometry based screening assay to measure epigenetic toxicity. MethodsX, 7():101055(2020) [pubmed]

10.6019/PXD019652;

10.1016/j.mex.2020.101055;

submitter keyword: Histone post-translational modifications, Drug safety, Toxicoepigenetics, Pharmacoepigenetics, Screening, Proteomics, LC-MS/MS

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, 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/2020/10/PXD019652

PRIDE project URI

• PRIDE
  1. PXD019652
     1. Label: PRIDE project
     2. Name: Comprehensive Histone Epigenetics (CHEpi): A mass spectrometry based screening assay to measure epigenetic toxicity