Proteomics

Dataset Information

0

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: PXD016308 | Pride | 2020-03-31

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
Ariadne_NME1_NCL1_rep1.csv Csv
Ariadne_NME1_NCL1_rep2.csv Csv
Ariadne_NME1_NCL1_rep3.csv Csv
Ariadne_NME1_control_rep1.csv Csv
Ariadne_NME1_control_rep2.csv Csv
Items per page:
1 - 5 of 43
altmetric image

Publications

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.

Wein Samuel S   Andrews Byron B   Sachsenberg Timo T   Santos-Rosa Helena H   Kohlbacher Oliver O   Kouzarides Tony T   Garcia Benjamin A BA   Weisser Hendrik H  

Nature communications 20200217 1

The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues within their sequence contexts. Mass spectrometry (MS) offers a comprehensive solution by using analogous approaches to shotgun proteomics. However, software support for the analysis of RNA MS data is inadequate at present and does not allow high-throughput processing. Exist  ...[more]

Similar Datasets

Proteomics MS-based analysis of enzymatic methylation of an in vitro-transcribed lncRNA
2018-12-31 | PXD012095 | Pride
Proteomics LC-MS/MS analysis of human long ribosomal RNA
2020-03-31 | PXD016323 | Pride
Proteomics LC-MS/MS analysis of human cellular tRNA
2020-03-31 | PXD016328 | Pride
Proteomics LC-MS/MS analysis of an intact synthetic microRNA
2019-01-10 | PXD012094 | Pride
Proteomics LC-MS/MS analysis of human cellular tRNA
2018-12-31 | PXD012097 | Pride
Proteomics Profiling 4-thiouridine across E. coli tRNAs
2022-01-30 | PXD028405 | Pride
Proteomics Human RNase 4 Improves mRNA Sequence Characterization by LC-MS/MS.
2022-07-26 | PXD033334 | Pride
Proteomics Elucidating the RNA-protein Interactomes of Target RNAs in Tissue
2023-07-30 | PXD038809 | Pride
Proteomics RNA oligomers training set for the Pytheas scoring function
2022-05-04 | PXD030435 | Pride
Proteomics Identification of proteins differentially associated with SARS CoV-2 subgenomic RNAs
2023-07-30 | PXD040147 | Pride