PXD066919

PXD066919 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometry-based Quantitative RNA Modification Mapping Using Isobaric Tandem Mass Tags
Description	Here, we present an RNA-specific isobaric tandem mass tagging (RMT) approach that enables the quantitative mapping of RNA modifications at an omics scale with high chemical accuracy. These RNA mass tags, derived and optimized from proteomics isobaric tags, are incorporated into an end-to-end workflow spanning sample preparation, LC-MS/MS acquisition, and customized data analysis. Validation using synthetic RNA oligonucleotides and total tRNAs from Pseudomonas aeruginosa UCBPP-PA14 outstanding quantification reproducibility, with coefficients of variation consistently below 5%. Applying this pipeline, we identified and quantified 22 RNA modifications in PA14 tRNAs, including two novel tRNA modification sites-m2A at position 38 and Gm/Cm at position 39-and their corresponding writer enzymes. Further analyses of tRNAs from writer enzyme knockout strains and cells cultured under stress conditions revealed dynamic modification patterns, interdependencies among modification pathways, novel insights into writer enzyme function and their potential roles in cellular stress adaptation. Our method provides a robust, and cost-effective platform for quantitative RNA modification mapping, enabling deeper biological insights and advancing RNA-related biomedical research.
HostingRepository	PRIDE
AnnounceDate	2026-07-01
AnnouncementXML	Submission_2026-06-30_19:56:22.301.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Junzhou Wu
SpeciesList	scientific name: Pseudomonas aeruginosa (strain UCBPP-PA14); NCBI TaxID: NEWT:208963;
ModificationList	iTRAQ4plex-116 reporter+balance reagent acylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-04 01:26:53	ID requested
⏵ 1	2026-06-30 19:56:22	announced

Dataset with its publication pending

submitter keyword: RNA modification, TMT, Tandem Mass tags, iTRAQ

Peter Dedon
contact affiliation	Massachusetts Institute of Technology
contact email	pcdedon@mit.edu
lab head
Junzhou Wu
contact affiliation	Singapore-MIT Alliance for Research and Technology Center
contact email	junzhou.wu@smart.mit.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/2026/07/PXD066919

PRIDE project URI

• PRIDE
  1. PXD066919
     1. Label: PRIDE project
     2. Name: Mass spectrometry-based Quantitative RNA Modification Mapping Using Isobaric Tandem Mass Tags