PXD064777

PXD064777 is an original dataset announced via ProteomeXchange.

Title	Evaluation of Protein Ion Relative Ratio Quantification in Top-down Electrospray Ionization–Mass Spectrometry Using Site-Specific Acetylated Recombinant Histone H3 Proteoforms
Description	Electrospray ionization (ESI)-mass spectrometry (MS) provides a crucial platform for analyzing post-translationally modified proteins. With continuous advances in MS instruments and data analysis approaches, analyzing intact proteoforms using a “top-down” approach has become highly feasible. To quantify proteoforms varied in post-translational modification (PTM), the PTMs’ influence on ESI-MS detection efficiency must be addressed. Two decades ago, the con-cept of using protein ion relative ratios (PIRRs) and fragment ion relative ratios (FIRRs) in ESI-MS for proteoform quantification was proposed by Kelleher and co-workers. Over these two decades, while FIRR quantification has been vigorously studied, the reliability of PIRR quantifi-cation, particularly for proteoforms varied in PTM extents, is relatively under-evaluated. In this study, using various site-specifically acetylated recombinant histone H3 proteoforms, the fidelity of PIRR quantification in top-down ESI-MS is further documented. Using an acetyllysine-amber stop codon orthogonal translation system, recombinant histone H3 carrying various number of acetylation were produced. They were subjected to absolute quantification using UV spectropho-tometry and combined in isometric ratio before analysis by either direct infusion-ESI-MS or weak cation exchange/hydrophilic interaction-ESI-MS. We report that all of the measured PIRRs closely reflect their theoretical ratios, regardless of acetylation extents and locations. These re-sults well supplement the supports on the validity of top-down proteoform quantification, partic-ularly for histone proteins.
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-28_22:49:43.441.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	acetylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-09 04:05:34	ID requested
⏵ 1	2025-09-28 22:49:44	announced

10.1021/jasms.5c00079;

Lui KW, Ngai SM, Chan TF, Evaluation of Protein Ion Relative Ratio Quantification in Top-down Electrospray Ionization-Mass Spectrometry Using Site-Specific Acetylated Recombinant Histone H3 Proteoforms. J Am Soc Mass Spectrom, 36(10):2048-2058(2025) [pubmed]

submitter keyword: proteoforms,Top-down proteomics, histone H3, quantitative proteomics, protein ion relative ratio

Ting Fung Chan
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	tf.chan@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/2025/09/PXD064777

PRIDE project URI

• PRIDE
  1. PXD064777
     1. Label: PRIDE project
     2. Name: Evaluation of Protein Ion Relative Ratio Quantification in Top-down Electrospray Ionization–Mass Spectrometry Using Site-Specific Acetylated Recombinant Histone H3 Proteoforms