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MS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Hendrik Weisser

LAB HEAD: Byron Andrews

PROVIDER: PXD012095 | Pride | 2018-12-31

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Ariadne_NME1_NCL1.csv	Csv
	Ariadne_NME1_control.csv	Csv
	LFQ_NME1_NCL1_FDR1.csv	Csv
	LFQ_NME1_NCL1_FDR1.featureXML.xml	Xml
	LFQ_NME1_control_FDR1.csv	Csv

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MS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA

Project 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.

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