PXD026820

PXD026820 is an original dataset announced via ProteomeXchange.

Title	A PrSM-level Side-by-Side Comparison of On-line LCMS methods on Intact Histone H3 and H4 Proteoforms
Description	The heterogeneity of histone H3 proteoforms has made histone H3 top-down analysis challenging. To enhance the detection coverage on the proteoforms, performing liquid chromatography (LC) front-end to MS detection is recommended. Here, by using optimized Electron-Transfer/High-Energy Collision Dissociation (EThcD) parameters, we have conducted a proteoform-spectrum match (PrSM) level side-by-side comparison on reversed-phase LC-MS (RPLC-MS), ‘Dual Gradient’ Weak Cation Exchange/Hydrophilic Interaction LC-MS (Dual Gradient WCX/HILIC-MS) and ‘Organic Rich’ WCX/HILIC-MS, on the top-down analysis of H3.1, H3.2 and H4 proteins extracted from HeLa cell culture. While both Dual Gradient WCX/HILIC and Organic Rich WCX/HILIC could resolve intact H3 and H4 proteoforms by the number of acetylations, the Organic Rich method could enhance the separations of different trimethyl/acetyl near-isobaric H3 proteoforms. In comparison with RPLC-MS, both of the WCX/HILIC-MS methods had enormously enhanced the qualities of the H3 PrSMs and remarkably improved the range, reproducibility, and confidence in the identifications of H3 proteoforms.
HostingRepository	PRIDE
AnnounceDate	2025-03-03
AnnouncementXML	Submission_2025-03-03_02:49:39.387.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kin Wing Lui
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; dihydroxylated residue; phosphorylated residue; N6; acetylated residue; monohydroxylated residue; dimethylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-20 22:53:54	ID requested
⏵ 1	2025-03-03 02:49:40	announced

10.1021/acs.jproteome.1c00308;

Lui KW, Ngai SM, PrSM-Level Side-by-Side Comparison of Online LC-MS Methods with Intact Histone H3 and H4 Proteoforms. J Proteome Res, 20(9):4331-4345(2021) [pubmed]

submitter keyword: top-down proteomics, histones, post-translation modifications, on-line LCMS, RPLC, ESI-Compatible WCX/HILIC

Sai-Ming Ngai
contact affiliation	School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong.
contact email	smngai@cuhk.edu.hk
lab head
Kin Wing Lui
contact affiliation	The Chinese University of Hong Kong
contact email	1155064778@link.cuhk.edu.hk
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/2025/03/PXD026820

PRIDE project URI

• PRIDE
  1. PXD026820
     1. Label: PRIDE project
     2. Name: A PrSM-level Side-by-Side Comparison of On-line LCMS methods on Intact Histone H3 and H4 Proteoforms