PXD053212

PXD053212 is an original dataset announced via ProteomeXchange.

Title	An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS
Description	The eukaryotic genome is packaged around histone proteins, which are subject to a myriad of post-translational modifications. By controlling DNA accessibility and the recruitment of protein complexes that mediate chromatin-related processes, these modifications constitute a key mechanism of epigenetic regulation. Since mass spectrometry can easily distinguish between these different modifications, it has become an essential technique in deciphering the histone code. Although robust LC-MS/MS methods are available to analyze modifications on the histone N-terminal tails, routine methods for characterizing ubiquitin marks on histone C-terminal regions, especially H2AK119ub, are less robust. Here we report the development of a simple workflow for the detection and improved quantification of the canonical histone ubiquitination marks H2AK119ub and H2BK120ub. The method entails a fully tryptic digestion of acid-extracted histones followed by derivatization with heavy or light propionic anhydride. A pooled sample is then spiked into oppositely labeled single samples as a reference channel for relative quantification, and data is acquired using PRM-based nanoLC-MS/MS. We validated our approach with synthetic peptides as well as treatments known to modulate the levels of H2AK119ub and H2BK120ub. This new method complements existing histone workflows, largely focused on the lysine-rich N-terminal regions, by extending modification analysis to other sequence contexts.
HostingRepository	PanoramaPublic
AnnounceDate	2024-12-10
AnnouncementXML	Submission_2024-12-10_15:09:10.633.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Peder Lund
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	GG; Propionyl; Label:13C(6)15N(1); Label:13C(5)15N(1)
Instrument	Q Exactive; Q Exactive HF; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-18 13:55:45	ID requested
1	2024-10-19 21:08:24	announced
⏵ 2	2024-12-10 15:09:11	announced	: Added PubMed Id

Lopes M, Lund PJ, Garcia BA, Optimized and Robust Workflow for Quantifying the Canonical Histone Ubiquitination Marks H2AK119ub and H2BK120ub by LC-MS/MS. J Proteome Res, 23(12):5405-5420(2024) [pubmed]

submitter keyword: Histones, post-translational modifications, ubiquitination, epigenetics, LC-MS/MS

Benjamin A. Garcia
contact affiliation	Dept. of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis
contact email	bagarcia@wustl.edu
lab head
Peder Lund
contact affiliation	Case Western Reserve University
contact email	pxl446@case.edu
dataset submitter

Panorama Public dataset URI