PXD074730-1

PXD074730 is an original dataset announced via ProteomeXchange.

Title	Proton Transfer Charge Reduction Enables Isobaric Labeling-Based Proteoform Quantification of Overlapping Signals in Top-Down Mass Spectrometry
Description	Top-down mass spectrometry provides a powerful approach for analyzing and quantifying intact proteoforms, i.e., the distinct molecular forms of proteins. Isobaric labeling-based quantification strategies offer the advantages of multiplexing and increased analytical depth. However, a major challenge remains the quantification of proteoforms when their precursor signals overlap, leading to mixed reporter ion intensities. In this proof-of-concept study, we employed proton transfer charge reduction (PTCR) at the MS2 level to resolve overlapping precursor signals, allowing selective isolation of individual proteoforms and subsequently, their accurate reporter ion quantification at the MS3 level. Using direct infusion mass spectrometry of model proteins labeled with cysteine-directed tandem mass tags, we demonstrate that this approach enables accurate, interference-free reporter ion-based quantification in the presence of overlapping proteoforms and spectrally congested backgrounds. This work highlights PTCR as a versatile gas-phase separation strategy to enhance the quantitative capabilities of labeling-based top-down mass spectrometry, offering a path toward precise, proteoform-resolved quantification across diverse experimental approaches.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-08_01:27:04.264.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Tholey
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: NEWT:9031; scientific name: Bos taurus (Bovine); NCBI TaxID: NEWT:9913;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-23 01:43:57	ID requested
⏵ 1	2026-06-08 01:27:05	announced

Kaulich PT, Tholey A, Proton Transfer Charge Reduction Enables Isobaric Labeling-Based Proteoform Quantification of Overlapping Signals in Top-Down Mass Spectrometry. J Am Soc Mass Spectrom, 37(5):1289-1294(2026) [pubmed]

10.1021/jasms.6c00060;

submitter keyword: Proton transfer charge reduction, top-down proteomics, isobaric labeling, proteoform, quantification

Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
contact email	a.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, University of Kiel
contact email	a.tholey@iem.uni-kiel.de
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/2026/06/PXD074730

PRIDE project URI

• PRIDE
  1. PXD074730
     1. Label: PRIDE project
     2. Name: Proton Transfer Charge Reduction Enables Isobaric Labeling-Based Proteoform Quantification of Overlapping Signals in Top-Down Mass Spectrometry