PXD016308-1

PXD016308 is an original dataset announced via ProteomeXchange.

Title	MS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA
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 prepared two samples of an in vitro-transcribed yeast lncRNA (NME1, 340 nt long), one of which was treated with an RNA methyltransferase (NCL1) catalyzing the 5-methylcytidine (m5C) modification. These samples were subsequently digested with an RNA endonuclease (RNase) to generate oligonucleotide sequences of a length amenable to mass spectrometry.
HostingRepository	PRIDE
AnnounceDate	2020-03-31
AnnouncementXML	Submission_2020-03-31_04:48:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hendrik Weisser
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monomethylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-18 01:40:46	ID requested
⏵ 1	2020-03-31 04:48:42	announced
2	2024-10-22 05:01:28	announced	2024-10-22: Updated project metadata.

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]

submitter keyword: RNA, lncRNA, epitranscriptomics, NME1, m5C, 5-methylcytidine

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

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/PXD016308

PRIDE project URI

• PRIDE
  1. PXD016308
     1. Label: PRIDE project
     2. Name: MS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA