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PXD016308-1

PXD016308 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2020-03-31
AnnouncementXMLSubmission_2020-03-31_04:48:41.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterHendrik Weisser
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListmonomethylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-11-18 01:40:46ID requested
12020-03-31 04:48:42announced
Publication List
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, lncRNA, epitranscriptomics, NME1, m5C, 5-methylcytidine
Contact List
Byron Andrews
contact affiliationSTORM Therapeutics Limited, Cambridge, United Kingdom
contact emailbyron.andrews@stormtherapeutics.com
lab head
Hendrik Weisser
contact affiliationSTORM Therapeutics Limited
contact emailhendrik.weisser@stormtherapeutics.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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