RNAModMapper: RNA Modification Mapping Software for Analysis of Liquid Chromatography Tandem Mass Spectrometry Data.

Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven to be a powerful analytical tool for the characterization of modified ribonucleic acids (RNAs). The typical approach for analyzing modified nucleosides within RNA sequences by mass spectrometry involves ribonuclease digestion followed by LC-MS/MS analysis and data interpretation. Here we describe a new software tool, RNAModMapper (RAMM), to assist in the interpretation of LC-MS/MS data. RAMM is a stand-alone package that requires user-submitted DNA or RNA sequences to create a local database against which collision-induced dissociation (CID) data of modified oligonucleotides can be compared. RAMM can interpret MS/MS data containing modified nucleosides in two modes: fixed and variable. In addition, RAMM can also utilize interpreted MS/MS data for RNA modification mapping back against the input sequence(s). The applicability of RAMM was first tested using total tRNA isolated from Escherichia coli. It was then applied to map modifications found in 16S and 23S rRNA from Streptomyces griseus.

[1]  T. Uchida,et al.  Specificity of RNase U2. , 1970, Journal of biochemistry.

[2]  Jef Rozenski,et al.  The RNA modification database, RNAMDB: 2011 update , 2010, Nucleic Acids Res..

[3]  K. Entian,et al.  Absolute and relative quantification of RNA modifications via biosynthetic isotopomers , 2014, Nucleic acids research.

[4]  Pietro Traldi,et al.  Rapid Commun. Mass Spectrom.10. 1629-1637 (1996) Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry in Milk Science , 1997 .

[5]  Yuri Motorin,et al.  High-throughput sequencing for 1-methyladenosine (m(1)A) mapping in RNA. , 2016, Methods.

[6]  Robert Burke,et al.  ProteoWizard: open source software for rapid proteomics tools development , 2008, Bioinform..

[7]  E. Phizicky,et al.  Do all modifications benefit all tRNAs? , 2010, FEBS letters.

[8]  J. McCloskey,et al.  [44] Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry , 1990 .

[9]  P. Limbach,et al.  RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids , 2015, Nucleic acids research.

[10]  Michael A. Freitas,et al.  MassMatrix: A database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data , 2009, Proteomics.

[11]  T. Carell,et al.  Parallel isotope-based quantification of modified tRNA nucleosides. , 2009, Angewandte Chemie.

[12]  B. C. Persson.  Modification of tRNA as a regulatory device , 1993, Molecular microbiology.

[13]  P. Limbach,et al.  Mass spectrometry of modified RNAs: recent developments. , 2016, The Analyst.

[14]  Rune Matthiesen,et al.  Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping , 2009, Nucleic acids research.

[15]  Patricia P. Chan,et al.  GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes , 2015, Nucleic Acids Res..

[16]  J. Kowalak,et al.  A novel method for the determination of post-transcriptional modification in RNA by mass spectrometry. , 1993, Nucleic acids research.

[17]  F. Kirpekar,et al.  Detection of pseudouridine and other modifications in tRNA by cyanoethylation and MALDI mass spectrometry. , 2002, Nucleic acids research.

[18]  Chia-Yu Yen,et al.  Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library* , 2011, Molecular & Cellular Proteomics.

[19]  P. Limbach,et al.  Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC-UV-MS. , 2013, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[20]  M. Esteller.  Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.

[21]  Gary L. Glish,et al.  Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides , 1992, Journal of the American Society for Mass Spectrometry.

[22]  P. Limbach,et al.  Combining recombinant ribonuclease U2 and protein phosphatase for RNA modification mapping by liquid chromatography-mass spectrometry. , 2015, Analytical biochemistry.

[23]  Yoshiyuki Kuchino,et al.  Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification , 1988, Nature.

[24]  P. Limbach,et al.  Summary: the modified nucleosides of RNA. , 1994, Nucleic acids research.

[25]  P. Limbach,et al.  Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia , 2015, RNA.

[26]  P. Limbach,et al.  Removal of 3'-phosphate group by bacterial alkaline phosphatase improves oligonucleotide sequence coverage of RNase digestion products analyzed by collision-induced dissociation mass spectrometry. , 2011, Rapid communications in mass spectrometry : RCM.

[27]  P. Limbach,et al.  Enhanced Detection of Post-Transcriptional Modifications Using a Mass-Exclusion List Strategy for RNA Modification Mapping by LC-MS/MS , 2015, Analytical chemistry.

[28]  S. A. McLuckey,et al.  Decompositions of multiply charged oligonucleotide anions , 1993 .

[29]  J. Steyaert.  A decade of protein engineering on ribonuclease T1--atomic dissection of the enzyme-substrate interactions. , 1997, European journal of biochemistry.

[30]  P. Limbach,et al.  Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. , 2016, Methods.

[31]  M. Helm,et al.  Analysis of RNA modifications by liquid chromatography-tandem mass spectrometry. , 2016, Methods.

[32]  Mark Helm,et al.  Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. , 2014, Chemistry & biology.

[33]  F. Arias,et al.  Cusativin, a new cytidine-specific ribonuclease accumulated in seeds of Cucumis sativus L. , 2004, Planta.

[34]  Misaki Akiyama,et al.  Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data , 2009, Nucleic acids research.

[35]  Chengqi Yi,et al.  Efficient and quantitative high-throughput transfer RNA sequencing , 2015, Nature Methods.

[36]  Clement T Y Chan,et al.  Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry , 2014, Nature Protocols.

[37]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[38]  P. Limbach,et al.  Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF* , 2016, The Journal of Biological Chemistry.

[39]  Gilbert S Omenn,et al.  An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis , 2005, Proteomics.

[40]  Clement T Y Chan,et al.  Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins , 2012, Nature Communications.

[41]  Jef Rozenski,et al.  SOS: A simple interactive program for ab initio oligonucleotide sequencing by mass spectrometry , 2002, Journal of the American Society for Mass Spectrometry.

[42]  G. Björk,et al.  Role of tRNA modification in translational fidelity. , 1990, Biochimica et Biophysica Acta.

[43]  Todd M. Lowe,et al.  ARM-Seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments , 2015, Nature Methods.

[44]  Jean-Louis Reymond,et al.  OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids , 2013, Journal of The American Society for Mass Spectrometry.

[45]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[46]  P. Limbach,et al.  Going global: the new era of mapping modifications in RNA , 2017, Wiley interdisciplinary reviews. RNA.

[47]  J. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways—2013 update , 2012, Nucleic Acids Res..

[48]  Takehiro Yasukawa,et al.  Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[49]  S. A. McLuckey,et al.  Ion trap collision-induced dissociation of multiply deprotonated RNA: c/y-ions versus (a-B)/w-ions , 2008, Journal of the American Society for Mass Spectrometry.