PXD030538

PXD030538 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Pytheas E. coli 16S rRNA sample analysis
Description	Mass spectrometry remains an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated into RNA therapeutics. To provide an analytical tool for sequence characterization of modified RNAs, we developed Pytheas, an open-source software package for automated analysis of tandem MS data for RNA. This dataset contains the analysis of 14N and 15N-labeled 16S RNA from E. coli, including all the known RNA modifications (excluding pseudouridines). The analysis has been performed using three different protocols and instruments: Agilent Q-TOF, Waters Synapt G2-S, and Thermo Scientific Orbitrap Fusion Lumos.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:37:38.731.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luigi D'Ascenzo
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Synapt MS; 6520A Quadrupole Time-of-Flight LC/MS

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-20 02:06:14	ID requested
⏵ 1	2024-10-08 11:37:39	announced

Publication List

10.1038/S41467-022-30057-5;
10.1038/s41467-022-30057-5;
D'Ascenzo L, Popova AM, Abernathy S, Sheng K, Limbach PA, Williamson JR, Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry. Nat Commun, 13(1):2424(2022) [pubmed]

10.1038/S41467-022-30057-5;

10.1038/s41467-022-30057-5;

D'Ascenzo L, Popova AM, Abernathy S, Sheng K, Limbach PA, Williamson JR, Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry. Nat Commun, 13(1):2424(2022) [pubmed]

Keyword List

submitter keyword: 16S,RNA, ribosome, isotope labeling, Pytheas

submitter keyword: 16S,RNA, ribosome, isotope labeling, Pytheas

Contact List

James R. Williamson
contact affiliation	Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
contact email	jrwill@scripps.edu
lab head
Luigi D'Ascenzo
contact affiliation	The Scripps Research Institute
contact email	dascenzoluigi@gmail.com
dataset submitter

Full Dataset Link List

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/2022/05/PXD030538
PRIDE project URI

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/2022/05/PXD030538

PRIDE project URI

Repository Record List

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