Improved application of RNAModMapper - An RNA modification mapping software tool - For analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data.
Alkaline Phosphatase
/ metabolism
Chromatography, Liquid
/ statistics & numerical data
Data Interpretation, Statistical
Oligoribonucleotides
/ analysis
RNA Processing, Post-Transcriptional
RNA, Transfer, Phe
/ analysis
Ribonuclease T1
/ metabolism
Saccharomyces cerevisiae
Sequence Analysis, RNA
/ statistics & numerical data
Software
Tandem Mass Spectrometry
/ statistics & numerical data
Bioinformatics
Modification placement
Modified nucleosides
Sequence analysis
Transfer RNA
Journal
Methods (San Diego, Calif.)
ISSN: 1095-9130
Titre abrégé: Methods
Pays: United States
ID NLM: 9426302
Informations de publication
Date de publication:
01 03 2019
01 03 2019
Historique:
received:
03
08
2018
revised:
02
10
2018
accepted:
21
10
2018
pubmed:
27
10
2018
medline:
21
11
2019
entrez:
27
10
2018
Statut:
ppublish
Résumé
Research into post-transcriptional processing and modification of RNA continues to speed forward, as their ever-emerging role in the regulation of gene expression in biological systems continues to unravel. Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven for over two decades to be a powerful ally in the elucidation of RNA modification identity and location, but the technique has not proceeded without its own unique technical challenges. The throughput of LC-MS/MS modification mapping experiments continues to be impeded by tedious and time-consuming spectral interpretation, particularly during for the analysis of complex RNA samples. RNAModMapper was recently developed as a tool to improve the interpretation and annotation of LC-MS/MS data sets from samples containing post-transcriptionally modified RNAs. Here, we delve deeper into the methodology and practice of RNAModMapper to provide greater insight into its utility, and remaining hurdles, in current RNA modification mapping experiments.
Identifiants
pubmed: 30366097
pii: S1046-2023(18)30174-9
doi: 10.1016/j.ymeth.2018.10.012
pmc: PMC6397789
mid: NIHMS1511167
pii:
doi:
Substances chimiques
Oligoribonucleotides
0
RNA, Transfer, Phe
0
Ribonuclease T1
EC 3.1.27.3
Alkaline Phosphatase
EC 3.1.3.1
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
128-138Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM058843
Pays : United States
Organisme : NIGMS NIH HHS
ID : R56 GM058843
Pays : United States
Informations de copyright
Copyright © 2018 Elsevier Inc. All rights reserved.
Références
Nucleic Acids Res. 2002 Dec 1;30(23):e135
pubmed: 12466567
Cell. 2014 Sep 25;159(1):148-162
pubmed: 25219674
Biochemistry. 1997 Jul 8;36(27):8269-75
pubmed: 9204872
J Am Soc Mass Spectrom. 2013 Feb;24(2):249-56
pubmed: 23264149
Cell Mol Life Sci. 2018 Jan;75(2):241-260
pubmed: 28752201
Genes Cells. 2002 Mar;7(3):259-72
pubmed: 11918670
Methods Mol Biol. 2009;492:143-60
pubmed: 19241031
RNA. 2015 Oct;21(10):1746-56
pubmed: 26221047
Methods Enzymol. 2015;560:29-71
pubmed: 26253965
Anal Bioanal Chem. 2017 Sep;409(24):5645-5654
pubmed: 28730304
Enzymes. 2017;41:1-50
pubmed: 28601219
Nucleic Acids Res. 1993 Sep 25;21(19):4577-85
pubmed: 8233793
Nucleic Acids Res. 1998 Jan 1;26(1):148-53
pubmed: 9399820
Nat Rev Mol Cell Biol. 2017 Mar;18(3):202-210
pubmed: 28144031
J Am Soc Mass Spectrom. 1994 Aug;5(8):740-7
pubmed: 24222001
Nucleic Acids Res. 2001 May 15;29(10):E49-9
pubmed: 11353094
J Am Soc Mass Spectrom. 2008 Dec;19(12):1832-40
pubmed: 18799321
Methods. 2016 Sep 1;107:110-21
pubmed: 26922842
Nucleic Acids Res. 2015 May 26;43(10):e64
pubmed: 25820423
Nat Chem Biol. 2016 May;12(5):311-6
pubmed: 26863410
Nucleic Acids Res. 2006 Feb 01;34(2):721-33
pubmed: 16452298
J Chromatogr A. 2019 Jun 21;1595:39-48
pubmed: 30772056
Nucleic Acids Res. 2018 Jan 4;46(D1):D303-D307
pubmed: 29106616
Methods. 2016 Sep 1;107:73-8
pubmed: 27033178
J Am Soc Mass Spectrom. 2002 Mar;13(3):200-3
pubmed: 11908799
Annu Rev Biochem. 1987;56:263-87
pubmed: 3304135
Nucleic Acids Res. 2009 Apr;37(6):e47
pubmed: 19270066
Nucleic Acids Res. 2009 Apr;37(6):e48
pubmed: 19264806
Mol Cell Proteomics. 2011 Jul;10(7):M111.007666
pubmed: 21532008
J Biol Chem. 1948 Aug;175(1):315-32
pubmed: 18873306
Nat Biotechnol. 2006 Oct;24(10):1285-92
pubmed: 16964243
J Am Soc Mass Spectrom. 1992 Jan;3(1):60-70
pubmed: 24242838
Nat Rev Genet. 2017 May;18(5):275-291
pubmed: 28216634
Cell. 2017 Jun 15;169(7):1187-1200
pubmed: 28622506
Anal Chem. 1996 Jul 1;68(13):1989-99
pubmed: 9027217
Anal Chem. 2017 Oct 17;89(20):10744-10752
pubmed: 28942636