PXD069039-1

PXD069039 is an original dataset announced via ProteomeXchange.

Title	Multiplexed quantitation of post-translational modified peptides in single cells using triggered MS/MS combined with super heavy tandem mass tags
Description	Recent advances in mass spectrometry now allow unbiased proteome profiling of thousands of proteins from single cells using both label-free and labeling approaches. However, a major limitation of unbiased approaches is missing data, which worsens as the sample size increases. In addition, the reproducible measurement of post-translational modifications (PTMs) at the single cell level, particularly those present at lower stoichiometry than their unmodified counterparts, remains an even greater challenge. To overcome this issue, we developed a targeted strategy that combines tandem mass tag (TMT) multiplexing with SureQuant-based triggered MS/MS using super heavy TMT-labeled peptides that are 9 Da heavier than the TMTpro tags as triggers. To showcase the strength of our approach, we established a method quantifying four PTMs of histone H3 (i.e., K14ac, K27me, K27me3, and K79me) at single cell resolution. We demonstrated the robustness in quantitation compared to conventional approaches of data-dependent acquisition and standard parallel reaction monitoring with analytical throughput of 1,080 single cells per day. Furthermore, we applied this strategy to sorted single cells and revealed cellular heterogeneity in histone PTMs. Overall, we developed the targeted strategy with improved sensitivity and throughput for analyzing PTMs in single cells, which we expect will be broadly applicable to multiple types of PTMs while enabling focused analysis.
HostingRepository	PRIDE
AnnounceDate	2025-12-15
AnnouncementXML	Submission_2025-12-14_16:15:14.713.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monomethylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-01 11:16:50	ID requested
⏵ 1	2025-12-14 16:15:15	announced

van Dieren A, Bittner A, Wurzinger B, Afjehi-Sadat L, Weckwerth W, Teige M, Vothknecht UC, -dependent and -independent changes in response to oxidative stress in Arabidopsis thaliana. Planta, 263(1):23(2025) [pubmed]

10.1007/s00425-025-04891-y;

submitter keyword: PTM, SureQuant,Single cell proteomics, Super heavy tandem mass tags

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
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/2025/12/PXD069039

PRIDE project URI

• PRIDE
  1. PXD069039
     1. Label: PRIDE project
     2. Name: Multiplexed quantitation of post-translational modified peptides in single cells using triggered MS/MS combined with super heavy tandem mass tags