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PXD030538

PXD030538 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePytheas E. coli 16S rRNA sample analysis
DescriptionMass 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-08
AnnouncementXMLSubmission_2024-10-08_11:37:38.731.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLuigi D'Ascenzo
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion Lumos; Synapt MS; 6520A Quadrupole Time-of-Flight LC/MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-12-20 02:06:14ID requested
12024-10-08 11:37:39announced
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]
Keyword List
submitter keyword: 16S,RNA, ribosome, isotope labeling, Pytheas
Contact List
James R. Williamson
contact affiliationDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
contact emailjrwill@scripps.edu
lab head
Luigi D'Ascenzo
contact affiliationThe Scripps Research Institute
contact emaildascenzoluigi@gmail.com
dataset submitter
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Dataset FTP location
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