PXD028269

PXD028269 is an original dataset announced via ProteomeXchange.

Title	Chemical derivatization of histones for LC-MS/MS analysis
Description	Histone lysine methylation is an important post-translational modifications (PTMs) that plays critical roles in numerous biological processes with abnormal histone lysine methylation having been associated with developmental defects and human diseases. The primary amine of all lysine residues can be mono-, di-, or trimethylated and the extent of methylation at a single site is shown to inspire unique protein function. Moreover, histone lysine methylation can activate or repress transcription depending on which sites are modified and to what degree. Therefore, a comprehensive stoichiometric analysis of histone lysine methylation is necessary to fully elucidate its function. As histones are lysine-rich and highly-hydrophilic proteins (Figure S1), trypsin digestion of histones results in small, hydrophilic peptides which often suffer from substantial losses during sample preparation, and are difficult to detect in conventional reversed phase LC-MS. Additionally, trypsin fails to cleave histone proteins when lysine residues are methylated, resulting in inaccurate estimations of site occupancy and methylation extent. Previously, lysine propionylation labeling has been developed to overcome this drawback and facilitate quantitative analysis of PTMs that frequently occur on the lysine residue of histones. However, propionylation labeling of unmodified and monomethylated lysine residues causes a mismatch in hydrophobicity and charge state between labeled and unlabeled di-/trimethylated peptides. This mismatch forces retention time and signal intensity differences that inspire inaccurate quantitation and miscalculation of site occupancy. In this work, we developed a method that facilitates blocking of free lysine groups and discrimination of native lysine methylation, enables accurate calculation of the histone lysine methylation stoichiometry.
HostingRepository	PRIDE
AnnounceDate	2022-05-25
AnnouncementXML	Submission_2022-05-25_05:06:16.257.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Junfeng Huang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 08:00:19	ID requested
⏵ 1	2022-05-25 05:06:17	announced

Chan NT, Huang J, Ma G, Zeng H, Donahue K, Wang Y, Li L, Xu W, The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium. Nucleic Acids Res, 50(4):1969-1992(2022) [pubmed]

submitter keyword: Histone, propionylation, dimethyl labeling, histione methylation

Lingjun Li
contact affiliation	School of Pharmacy, University of Wisconsin-Madison
contact email	lingjun.li@wisc.edu
lab head
Junfeng Huang
contact affiliation	University of Wisconsin-Madison
contact email	jhuang373@wisc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028269
     1. Label: PRIDE project
     2. Name: Chemical derivatization of histones for LC-MS/MS analysis