PXD061704-1

PXD061704 is an original dataset announced via ProteomeXchange.

Title	Toward standardized epitranscriptome analytics: An inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA
Description	The human RNome comprises all forms of RNA and the 50+ chemical structures – the epitranscriptome – that modify them. Understanding the diverse functions of RNA modifications in regulating gene expression and cell phenotype requires technologies such as RNA sequencing-based modification mapping and mass spectrometry-based quantification of modified ribonucleosides. Liquid chromatography-coupled tandem quadrupole mass spectrometry (LC-MS/MS) is the gold standard for detecting and quantifying all modified ribonucleosides in a sample with accuracy and precision. However, variations in RNA isolation, processing, and LC-MS/MS analysis have hindered reproducibility across laboratories, which is essential for accurate quantification of RNA modifications. Here we report a multi-laboratory effort to optimize and standardize the workflow for LC-MS/MS RNA modification analysis. We compared protocols for sample shipment, RNA digestion, LC-MS/MS analysis, and data processing among three laboratories working with the same total RNA samples.
HostingRepository	PRIDE
AnnounceDate	2025-09-12
AnnouncementXML	Submission_2025-09-12_08:25:06.457.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chi Kong Chan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	6460 Triple Quadrupole LC/MS; 6495C Triple Quadrupole LC/MS; TSQ Quantiva

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-11 08:02:37	ID requested
⏵ 1	2025-09-12 08:25:06	announced

10.1093/NAR/GKAF895;

submitter keyword: analytics,RNome, mass spectrometry, epitranscriptome, RNA

Peter C Dedon
contact affiliation	Underwood-Prescott Professor, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 56-731 Cambridge, MA 02139-4307
contact email	pcdedon@mit.edu
lab head
Chi Kong Chan
contact affiliation	Department of Biological Engineering, Massachusetts Institute of Technology
contact email	mckchan@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/2025/09/PXD061704

PRIDE project URI

• PRIDE
  1. PXD061704
     1. Label: PRIDE project
     2. Name: Toward standardized epitranscriptome analytics: An inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA