RoboOligo: Software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

Nucleic Acids Research

Volumn 43, Issue 10, 2015, Pages

  Sample, Paul J ^a   Gaston, Kirk W ^b   Alfonzo, Juan D ^a   Limbach, Patrick A ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGOMER; RNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; COLLISION INDUCED DISSOCIATION TANDEM MASS SPECTROMETRY; COLLISIONALLY ACTIVATED DISSOCIATION; COMPUTER PROGRAM; CONTROLLED STUDY; DE NOVO SEQUENCING; DNA MODIFICATION; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA HYBRIDIZATION; RNA SEQUENCE; TANDEM MASS SPECTROMETRY; ALGORITHM; CHEMISTRY; METABOLISM; PROCEDURES; RNA PROCESSING; SEQUENCE ANALYSIS;

ALGORITHMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84931292139     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv145     Document Type: Article

References (54)

1. Sanger, F. and Coulson, A.R. (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol., 94, 441-448.
2. Machnicka, M.A., Milanowska, K., Osman Oglou, O., Purta, E., Kurkowska, M., Olchowik, A., Januszewski, W., Kalinowski, S., Dunin-Horkawicz, S., Rother, K.M. et al. (2013) MODOMICS: a database of RNA modifcation pathways-2013 update. Nucleic Acids Res., 41, D262-D267.
3. Cantara, W.A., Crain, P.F., Rozenski, J., McCloskey, J.A., Harris, K.A., Zhang, X., Vendeix, F.A., Fabris, D. and Agris, P.F. (2011) The RNA modifcation database, RNAMDB: 2011 update. Nucleic Acids Res., 39, D195-D201.
4. Huber, C.G. and Oberacher, H. (2001) Analysis of nucleic acids by on-line liquid chromatography-Mass spectrometry. Mass Spectrom. Rev., 20, 310-343.
5. McCloskey, J., Whitehill, A., Rozenski, J., Qiu, F. and Crain, P. (1999) New techniques for the rapid characterization of oligonucleotides by mass spectrometry. Nucleosides Nucleotides, 18, 1549-1553.
6. McLuckey, S.A. and Habibi-Goudarzi, S. (1993) Decompositions of multiply charged oligonucleotide anions. J. Am. Chem. Soc., 115, 12085-12095.
7. McLuckey, S.A., Van Berker, G.J. and Glish, G.L. (1992) Tandem mass spectrometry of small, multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom., 3, 60-70.
8. Meng, Z. and Limbach, P.A. (2006) Mass spectrometry of RNA: linking the genome to the proteome. Brief Funct. Genomic Proteomic., 5, 87-95.
9. Wu, J. and McLuckey, S.A. (2004) Gas-phase fragmentation of oligonucleotide ions. Int. J. Mass Spectrom., 237, 197-241.
10. Tromp, J.M. and Schürch, S. (2005) Gas-phase dissociation of oligoribonucleotides and their analogs studied by electrospray ionization tandem mass spectrometry. J. Am. Soc. Mass Spectrom., 16, 1262-1268.
11. Monn, S.T.M. and Schürch, S. (2007) New aspects of the fragmentation mechanisms of unmodifed and methylphosphonate-modifed oligonucleotides. J. Am. Soc. Mass Spectrom., 18, 984-990.
12. Nyakas, A., Stucki, S.R. and Schürch, S. (2011) Tandem mass spectrometry of modifed and platinated oligoribonucleotides. J. Am. Soc. Mass Spectrom., 22, 875-887.
13. Nordhoff, E., Kirpekar, F. and Roepstorff, P. (1996) Mass spectrometry of nucleic acids. Mass Spectrom. Rev., 15, 67-138.
14. Kowalak, J.A., Pomerantz, S.C., Crain, P.F. and McCloskey, J.A. (1993) A novel method for the determination of post-transcriptional modifcation in RNA by mass spectrometry. Nucleic Acids Res., 21, 4577-4585.
15. Nakayama, H., Takahashi, N. and Isobe, T. (2011) Informatics for mass spectrometry-based RNA analysis. Mass Spectrom. Rev., 30, 1000-1012.
16. Pomerantz, S.C., Kowalak, J.A. and McCloskey, J.A. (1993) Determination of oligonucleotide composition from mass spectrometrically measured molecular weight. J. Am. Soc. Mass Spectrom., 4, 204-209.
17. Rozenski, J. and McCloskey, J.A. (2002) SOS: a simple interactive program for ab initio oligonucleotide sequencing by mass spectrometry. J. Am. Soc. Mass Spectrom., 13, 200-203.
18. Nyakas, A., Blum, L.C., Stucki, S.R., Reymond, J.-L. and Schürch, S. (2013) OMA and OPA-software-supported mass spectra analysis of native and modifed nucleic acids. J. Am. Soc. Mass Spectrom., 24, 249-256.
19. Matthiesen, R. and Kirpekar, F. (2009) Identifcation of RNA molecules by specifc enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping. Nucleic Acids Res., 37, e48.
20. Nakayama, H., Akiyama, M., Taoka, M., Yamauchi, Y., Nobe, Y., Ishikawa, H., Takahashi, N. and Isobe, T. (2009) Ariadne: a database search engine for identifcation and chemical analysis of RNA using tandem mass spectrometry data. Nucleic Acids Res., 37, e47.
21. Kapp, E.A., Schütz, F., Connolly, L.M., Chakel, J.A., Meza, J.E., Miller, C.A., Fenyo, D., Eng, J.K., Adkins, J.N., Omenn, G.S. et al. (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specifcity analysis. Proteomics, 5, 3475-3490.
22. Muddiman, D.C, Anderson, G.A., Hofstadler, S.A. and Smith, R.D. (1997) Length and base composition of PCR-amplifed nucleic acids using mass measurements from electrospray ionization mass spectrometry. Anal. Chem., 69, 1543-1549.
23. Oberacher, H., Mayr, B.M. andHuber, C.G. (2004) Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry. J. Am. Soc. Mass Spectrom., 15, 32-42.
24. Oberacher, H. and Pitterl, F. (2011) Tandem mass spectrometric de novo sequencing of oligonucleotides using simulated annealing for stochastic optimization. Int. J. Mass Spectrom., 304, 124-129.
25. Oberacher, H., Wellenzohn, B. and Huber, C.G. (2002) Comparative sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry. Anal. Chem., 74, 211-218.
26. Liao, Q., Chiu, N.H., Shen, C, Chen, Y and Vouros, P. (2007) Investigation of enzymatic behavior of benzonase/alkaline phosphatase in the digestion of oligonucleotides and DNA by ESI-LC/MS. Anal. Chem., 79, 1907-1917.
27. Liao, Q., Shen, C. and Vouros, P. (2009) GenoMass-a computer software for automated identifcation of oligonucleotide DNA adducts from LC-MS analysis of DNA digests. J. Mass Spectrom., 44, 549-560.
28. Sharma, V.K., Glick, J., Liao, Q., Shen, C. and Vouros, P (2012) GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts. J. Mass Spectrom., 47, 490-501.
29. Kretschmer, M., Lavine, G, McArdle, J., Kuchimanchi, S., Murugaiah, V. and Manoharan, M. (2010) An automated algorithm for sequence confrmation of chemically modifed oligonucleotides by tandem mass spectrometry. Anal. Biochem., 405, 213-223.
30. Kirkpatrick, S., Gelatt, D Jr and Vecchi, M.P (1983) Optimization by simulated annealing. Science, 220, 671-680.
31. Menezes, S., Gaston, K.W., Krivos, K.L., Apolinario, E.E., Reich, NO., Sowers, K.R., Limbach, PA. and Perona, J.J. (2011) Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. Nucleic Acids Res., 39, 7641-7655.
32. Phillips, G, Swairjo, M.A., Gaston, K.W., Bailly, M., Limbach, PA., Iwata-Reuyl, D. and de CrÃcy-Lagard, V. (2012) Diversity of archaeosine synthesis in crenarchaeota. ACS Chem. Biol, 7, 300-305.
33. Rodriguez-Hernandez, A., Spears, J.L., Gaston, K.W., Limbach, PA., Gamper, H., Hou, Y.-M., Kaiser, R., Agris, PF. and Perona, J.J. (2013) Structural and mechanistic basis for enhanced translational effciency by 2-thiouridine at the tRNA anticodon wobble position. J. Mol. Biol, 425, 3888-3906.
34. Köhrer, C, Mandal, D., Gaston, K.W., Grosjean, H., Limbach, PA. and RajBhandary, U.L. (2014) Life without tRNAIle-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA2Ile. Nucleic Acids Res., 42, 1904-1915.
35. Puri, P, Wetzel, C, Saffert, P, Gaston, K.W., Russell, S.P, Varela, J.A.C, van der Vlies, P, Zhang, G, Limbach, PA., Ignatova, Z. et al. (2014) Systematic identifcation of tRNAome and its dynamics in Lactococcus lactis. Mol. Microbiol, 93, 944-956.
36. Spears, J., Gaston, K. and Alfonzo, J. (2011) In: Aphasizhev, R (ed). RNA and DNA Editing. Humana Press, Vol. 718, pp. 209-226.
37. Meng, Z. and Limbach, PA. (2004) RNase mapping of intact nucleic acids by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) and 18O labeling. Int. J. Mass Spectrom., 234, 37-44.
38. Steyaert, J. (1997) A decade of protein engineering on ribonuclease T1. Atomic dissection of the enzyme-substrate interactions. Eur. J. Biochem., 247, 1-11.
39. Krog, J.S., Espanol, Y, Giessing, A.M.B., Dziergowska, A., Malkiewicz, A., Pouplana, L.R. and Kirpekar, F (2011) 3-(3-amino-3-carboxypropyl)-5, 6-Dihydrouridine is one of two novel post-transcriptional modifcations in tRNA(Lys) (UUU) from Trypanosoma brucei. FEBS J., 278, 4782-4796.
40. Zallot, R., Brochier-Armanet, C, Gaston, K.W., Forouhar, F, Limbach, PA., Hunt, J.F and de Crecy-Lagard, V. (2014) Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem. Biol, 9, 1812-1825.
41. Grosjean, H. (2009) DNA and RNA Modifcation Enzymes: Structure, Mechanism, Function and Evolution. Landes Bioscience, Austin, TX.
42. Pomerantz, S.C. and McCloskey, J.A. (1990) Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol, 193, 796-824.
43. Gao, Y and McLuckey, S.A. (2012) Collision-induced dissociation of oligonucleotide anions fully modifed at the 2'-position of the ribose: 2'-F/-H and 2'-F/-H/-OMe mix-mers. J. Mass Spectrom., 47, 364-369.
44. Guymon, R., Pomerantz, S.C, Crain, PF and McCloskey, J.A. (2006) Infuence of phylogeny on posttranscriptional modifcation of rRNA in thermophilic prokaryotes: the complete modifcation map of 16S rRNA of Thermus thermophilus. Biochemistry, 45, 4888-4899.
45. Wong, S.Y, Javid, B., Addepalli, B., Piszczek, G, Strader, M.B., Limbach, PA. and Barry, CE. (2013) Functional role of methylation of G518 of the 16S rRNA 530 loop by GidB in Mycobacterium tuberculosis. Antimicrob. Agents Chemother, 57, 6311-6318.
46. Emmerechts, G, Barbé, S., Herdewijn, P, Anné, J. and Rozenski, J. (2007) Post-transcriptional modifcation mapping in the Clostridium acetobutylicum 16S rRNA by mass spectrometry and reverse transcriptase assays. Nucleic Acids Res., 35, 3494-3503.
47. Douthwaite, S. and Kirpekar, F (2007) Identifying modifcations in RNA by MALDI mass spectrometry. Methods Enzymol., 425, 3-20.
48. Schürch, S., Tromp, J. and Monn, S. (2007) Mass spectrometry of oligonucleotides. Nucleosides Nucleotides Nucleic Acids, 26, 1629-1633.
49. Medzihradszky, K.F and Chalkley, R.J. (2015) Lessons in de novo peptide sequencing by tandem mass spectrometry. Mass Spectrom. Rev., 34, 43-63.
50. Durairaj, A. and Limbach, PA. (2008) Mass spectrometry of the ffth nucleoside: a review of the identifcation of pseudouridine in nucleic acids. Anal. Chim. Acta, 623, 117-125.
51. Pomerantz, S.C and McCloskey, J.A. (2005) Detection of the common RNA nucleoside pseudouridine in mixtures of oligonucleotides by mass spectrometry. Anal. Chem., 77, 4687-4697.
52. Durairaj, A. and Limbach, PA. (2008) Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection. Anal Chim. Acta, 612, 173-181.
53. Mengel-Jørgensen, J. and Kirpekar, F. (2002) Detection of pseudouridine and other modifcations in tRNA by cyanoethylation and MALDI mass spectrometry. Nucleic Acids Res., 30, e 135.
54. Wetzel, C and Limbach, PA. (2013) The global identifcation of tRNA isoacceptors by targeted tandem mass spectrometry. Analyst, 138, 6063-6072.