PXD052972-1

PXD052972 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	PRIDE
AnnounceDate	2024-10-16
AnnouncementXML	Submission_2024-10-16_06:27:02.056.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD052972
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Peder Lund
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-10 12:28:29	ID requested
⏵ 1	2024-10-16 06:27:02	announced

10.6019/PXD052972;

submitter keyword: Histone post-translational modifications, H2AK119ub, H2BK120ub, ubiquitination

Benjamin A. Garcia
contact affiliation	Department of Biochemistry and Molecular Biophysics
contact email	bagarcia@wustl.edu
lab head
Peder Lund
contact affiliation	Case Western Reserve University
contact email	pederjlund@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD052972
     1. Label: PRIDE project
     2. Name: An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS