PXD016328

PXD016328 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	LC-MS/MS analysis of human cellular tRNA
Description	The field of epitranscriptomics is growing in importance, with chemical modification of RNA being associated with a wide variety of biological phenomena. Mass spectrometry (MS) enables the identification of modified RNA residues within their sequence contexts, by using analogous approaches to shotgun proteomics. We have developed a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), as part of the OpenMS software framework. NASE allows the reliable identification of (modified) RNA sequences from LC-MS/MS data in a high-throughput fashion. For this validation dataset, we generated samples of human total tRNA from a cellular extract - a complex mixture of highly modified RNAs. The samples were RNase-treated prior to nanoflow LC-MS/MS analysis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:29.049.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hendrik Weisser
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-18 09:02:31	ID requested
1	2020-03-31 04:49:32	announced
⏵ 2	2024-10-22 05:01:29	announced	2024-10-22: Updated project metadata.

Publication List

10.1038/s41467-020-14665-7;
Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H, A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nat Commun, 11(1):926(2020) [pubmed]

10.1038/s41467-020-14665-7;

Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H, A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nat Commun, 11(1):926(2020) [pubmed]

Keyword List

submitter keyword: RNA, tRNA, epitranscriptomics

submitter keyword: RNA, tRNA, epitranscriptomics

Contact List

Byron Andrews
contact affiliation	STORM Therapeutics Limited, Cambridge, United Kingdom
contact email	byron.andrews@stormtherapeutics.com
lab head
Hendrik Weisser
contact affiliation	STORM Therapeutics Limited
contact email	hendrik.weisser@stormtherapeutics.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/2020/03/PXD016328
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/2020/03/PXD016328

PRIDE project URI

Repository Record List

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