PXD051487

PXD051487 is an original dataset announced via ProteomeXchange.

Title	Linking acetyl-CoA labelling and histone acetylation dynamics for accurate determination of acetylation rates via ordinary differential equations
Description	To study complex biological systems, multi-omics methods have become an important tool. They integrate data from multiple biological layers, such as the metabolome and the proteome, to gain better insights of the processes happening. However, challenges remain both in sample preparation for measurements of different types of analytes as well as in the integration of different data types. Post-translational modifications such as acetylation of proteins are an example of a highly dynamic, reversible process that combines core metabolism with protein function. Histones are small proteins binding DNA that are highly acetylated in their N-terminal region. In this study, we utilise a simultaneous extraction method for acetyl-CoA and histones in combination with combined metabolic and chemical acetylation (CoMetChem) to track metabolic label incorporation into both acetyl-CoA and histones. Acetyl-CoA formation rates as well as histone acetylation- and deacetyation rates are modelled by ordinary differential equation, allowing the combination of data from acetyl-CoA and histone acetylation measurements into a unified model. We find that correcting for acetyl-CoA formation is necessary to accurately determine histone acetylation rates, particularly in systems with changes in upstream metabolism.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_14:40:42.591.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anna-Sophia Egger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-16 05:13:01	ID requested
⏵ 1	2025-05-06 14:40:43	announced

10.1016/j.molmet.2024.102032;

submitter keyword: Human, LC-MSMS, AcetylCoA, PTM, Histone, Acetylation, HEK93T

Marcel Kwiatkowski
contact affiliation	Functional Proteo-Metabolomics Institute of Biochemistry University of Innsbruck
contact email	marcel.kwiatkowski@uibk.ac.at
lab head
Anna-Sophia Egger
contact affiliation	Institut für Biochemie Universität Innsbruck
contact email	anna-sophia.egger@uibk.ac.at
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/2025/05/PXD051487

PRIDE project URI

• PRIDE
  1. PXD051487
     1. Label: PRIDE project
     2. Name: Linking acetyl-CoA labelling and histone acetylation dynamics for accurate determination of acetylation rates via ordinary differential equations