PXD071393

PXD071393 is an original dataset announced via ProteomeXchange.

Title	A Derivatization-Free PRM Workflow for Quantitative, Site-Specific Analysis of Histone Post-Translational Modifications
Description	Histone post-translational modifications (PTMs) are key regulators of chromatin architecture and gene expression. Although DIA-based platforms for histone PTM quantification are available, multiplexed targeted assays remain underdeveloped. In addition, bottom-up workflows frequently rely on chemical derivatization, which can introduce variability, increase procedural complexity, and obscure biologically relevant PTMs. Here, we present a derivatization-free parallel reaction monitoring (PRM) workflow for robust, quantitative, and site-specific analysis of histone PTMs. We employed highly efficient ArgC digestion to generate peptides of optimal length for LC–MS/MS without compromising endogenous PTMs, and we optimized chromatographic conditions to achieve isobaric separation and stable retention times. Co-eluting isobaric PTM species were confidently distinguished using site-specific fragment ions. The resulting PRM method enabled sensitive and reproducible detection of histone PTM isoforms across diverse biological systems. To illustrate its utility, we profiled PTM changes in cells expressing K-to-M mutations and in cells treated with the HDAC inhibitor entinostat, yielding results that correlated strongly with antibody-based assays. This PRM platform provides a practical and versatile framework for targeted analysis of histone PTMs identified across epigenetic studies.
HostingRepository	PRIDE
AnnounceDate	2026-09-09
AnnouncementXML	Submission_2026-09-09_03:09:23.786.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hyoungjoo Lee
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Bos taurus (Bovine); NCBI TaxID: NEWT:9913;
ModificationList	methylated residue; phosphorylated residue; acetylated residue; dimethylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-30 04:22:53	ID requested
⏵ 1	2026-09-09 03:09:31	announced

10.1021/acsomega.6c02411;

Lee H, Wiseman AK, Tibben BM, Sodiya I, Rothbart SB, Soper-Hopper MT, Sheldon RD, A Derivatization-Free Parallel Reaction Monitoring-Based Proteomics Workflow for Quantitative, Site-Specific Analysis of Histone Post-Translational Modifications. ACS Omega, 11(28):42597-42609(2026) [pubmed]

submitter keyword: PTMs, PRM, Skyline, Quantitation,Histone, ArgC

Ryan D. Sheldon
contact affiliation	Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
contact email	Ryan.Sheldon@vai.org
lab head
Hyoungjoo Lee
contact affiliation	Van Andel Institute
contact email	hyoungjoo.lee@vai.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD071393
     1. Label: PRIDE project
     2. Name: A Derivatization-Free PRM Workflow for Quantitative, Site-Specific Analysis of Histone Post-Translational Modifications