A Role for the MS Analysis of Nucleic Acids in the Post-Genomics Age

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 1, 2010, Pages 1-13

  Fabris, Daniele ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL STUDIES; BIOMEDICAL RESEARCH; DRUG DISCOVERY; GENOMICS; HUMAN GENOME PROJECT; HUMAN GENOMES; LIFE-SCIENCES; NEW APPLICATIONS; NUCLEIC ACID ANALYSIS; NUCLEIC ACID RESEARCH; RE-EVALUATION; SPECIFIC INTERACTION;

BIOMOLECULES; COMPUTER CRIME; GENES; MASS SPECTROMETERS; MASS SPECTROMETRY;

NUCLEIC ACIDS;

ARTICLE; CROSS LINKING; ELECTROSPRAY MASS SPECTROMETRY; GENETIC REGULATION; GENOMICS; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MEDICAL RESEARCH; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PROTEIN RNA BINDING; RIBOSWITCH; RNA PROCESSING; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

GENOMICS; HUMANS; MASS SPECTROMETRY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS;

EID: 73449100772     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2009.09.006     Document Type: Article

References (188)

1. Yamashita M., and Fenn J.B. Electrospray Ion Source. Another Variation on the Free-Jet Theme. J. Phys. Chem 88 (1984) 4671-4675
2. Aleksandrov M.L., Gall L.N., Krasnov V.N., Nikolaev V.I., Pavlenko V.A., and Shkurov V.A. Extraction of Ions from Solutions Under Atmospheric Pressure: A Method of Mass Spectrometric Analysis of Bioorganic Compounds. Doklady Akademii Nauk 277 (1984) 379-383
3. Tanaka K., Ido H., Yoshida Y., and Yoshida T. Detection of High Mass Molecules by Laser Desorption Time-of-Flight Mass Spectrometry. Proceedings of the Second Japan-China Joint Symposium on Mass Spectrometry (1987), Bando Press, Osaka, Osaka
4. Karas M., Bachmann D., Bahr U., and Hillenkamp F. Matrix-Assisted Ultraviolet Laser Desorption of Nonvolatile Compounds. Int. J. Mass Spectrom. Ion Processes 78 (1987) 53-68
5. Biemann K., and McCloskey J.A. Application of Mass Spectrometry to Structure Problems. VI. Nucleosides. J. Am. Chem. Soc 84 10 (1962) 2005-2007
6. Hattox S.E., and McCloskey J.A. Structure-Retention Relationships in the Gas Chromatography of Nucleosides. Anal. Chem 46 11 (1974) 1378-1383
7. McCloskey, J. A.; Lawson, A. M.; Tsuboyama, K.; Krueger, P. M.; Stillwell, R. N. Mass Spectrometry of Nucleic Acid Components. Trimethylsilyl Derivatives of Nucleotides, Nucleosides, and Bases. J. Am. Chem. Soc. 1068, 90(15), 4182-4184.
8. Lawson A.M., Stillwell R.N., Tacker M.M., Tsuboyama K., and McCloskey J.A. Mass Spectrometry of Nucleic Acid Components. Trimethylsilyl Derivatives of Nucleotides. J. Am. Chem. Soc 93 4 (1971) 1014-1023
9. 252Cf-Plasma Desorption Mass Spectrometry. Negative Ions of Dinucleoside Monophosphates. J. Am. Chem. Soc 104 (1982) 972-975
10. Grotjahn L., Frank R., and Blocker H. Ultrafast Sequencing of Oligodeoxyribonucleotides by FAB-Mass Spectrometry. Nucleic Acids Res 10 15 (1982) 4671-4678
11. Cerny R.L., Tomer K.B., Gross M.L., and Grotjahn L. Fast Atom Bombardment Combined with Tandem Mass Spectrometry for Determining Structures of Small Oligonucleotides. Anal. Biochem 165 1 (1987) 175-182
12. McCloskey J.A., and Nishimura S. Modified Nucleosides in Transfer RNA. Acc. Chem. Res 10 11 (1977) 403-410
13. Pang H., Smith D.L., Crain P.F., Yamaizumi K., Nishimura S., and McCloskey J.A. Identification of Nucleosides in Hydrolysates of Transfer RNA by High-Resolution Mass Spectrometry. Eur. J. Biochem 127 3 (1982) 459-471
14. McCloskey J.A. Structural Characterization of Natural Nucleosides by Mass Spectrometry. Acc. Chem. Res 24 3 (1991) 81-88
15. Lijinsky W., Loo J., and Ross A.E. Mechanism of Alkylation of Nucleic Acids by Nitrosodimethylamine. Nature 218 5147 (1968) 1174-1175
16. Cadet J., and Weinfeld M. Detecting DNA Damage. Anal, Chem 65 15 (1993) 675A-682A
17. Farmer P.B., and Sweetman G.M.A. Mass Spectrometric Detection of Carcinogen Adducts. J. Mass Spectrom 30 (1995) 1369-1379
18. Limbach P.A., Crain P.F., and McCloskey J.A. Summary: The Modified Nucleosides of RNA. Nucleic Acids Res 22 12 (1994) 2183-2196
19. Crain, P. F.; McCloskey, J. A. The RNA Modification Database. Nucleic Acids Res. 1007, 25(1), 126-127.
20. McCloskey J.A., and Crain P.F. The RNA Modification Database-1998. Nucleic Acids Res 26 1 (1998) 196-197
21. Apruzzese W.A., and Vouros P. Analysis of DNA Adducts by Capillary Methods Coupled to Mass Spectrometry: A Perspective. J. Chromatogr. A 794 1/2 (1998) 97-108
22. Tretyakova N., Matter B., Ogdie A., Wishnok J.S., and Tannenbaum S.R. Locating Nucleobase Lesions Within DNA Sequences by MALDI-TOF Mass Spectral Analysis of Exonuclease Ladders. Chem. Res. Toxicol 14 8 (2001) 1058-1070
23. Wang Y., Zhang Q., and Wang Y. Tandem Mass Spectrometry for the Determination of the Sites of DNA Interstrand Cross-Link. J. Am. Soc. Mass Spectrom 5 11 (2004) 1565-1571 1
24. Singh R., and Farmer P.B. Liquid Chromatography-Electrospray Ionization-Mass Spectrometry: The Future of DNA Adduct Detection. Carcinogenesis 27 2 (2006) 178-196
25. Kirpekar F., Nordhoff E., Kristiansen K., Roepstorff P., Lezius A., Hahner S., Karas M., and Hillenkamp F. Matrix Assisted Laser Desorption/Ionization Mass Spectrometry of Enzymatically Synthesized RNA up to 150 kDa. Nucleic Acids Res 22 19 (1994) 3866-3870
26. Tang K., Taranenko N.I., Allman S.L.L.Y., Chang L.Y., and Chen C.H. Detection of 500-Nucleotide DNA by Laser Desorption Mass Spectrometry. Rapid Commun. Mass Spectrom 8 (1994) 727-730
27. 8 Da by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem 67 (1995) 1159-1168
28. Muddiman D.C., Null A.P., and Hannis J.C. Precise Mass Measurement of a Double-Stranded 500 Base-Pair (309 kDa) Polymerase Chain Reaction Product by Negative Ion Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom 13 12 (1999) 1201-1204
29. Limbach P.A., Crain P.F., and McCloskey J.A. Characterization of Oligonucleotides and Nucleic Acids by Mass Spectrometry. Curr. Opin. Biotechnol 6 1 (1995) 96-102
30. Nordhoff E., Kirpekar F., and Roepstorff P. Mass Spectrometry of Nucleic Acids. Mass Spectrom. Rev 15 (1996) 67-138
31. Banoub J.H., Newton R.P., Esmans E., Ewing D.F., and Mackenzie G. Recent Developments in Mass Spectrometry for the Characterization of Nucleosides, Nucleotides, Oligonucleotides, and Nucleic Acids. Chem. Rev 105 5 (2005) 1869-1915
32. Frahm J.L., and Muddiman D.C. Nucleic Acid Analysis by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at the Beginning of the Twenty-First Century. Curr. Pharm. Des 11 20 (2005) 2593-2613
33. Hofstadler S.A., Sannes-Lowery K.A., and Hannis J.C. Analysis of nucleic acids by FTICR MS. Mass Spectrom. Rev 24 (2005) 265-285
34. National Research Council. Mapping and Sequencing the Human Genome (1988), National Academy Press, Washington, DC
35. Watson J.D., and Jordan E. The Human Genome Program at the National Institutes of Health. Genomics 5 3 (1989) 654-656
36. McLuckey S.A., and Habibi-Goudarzi S. Decompositions of Multiply Charged Oligonucleotide Anions. J. Am. Chem. Soc 115 (1993) 12085-12095
37. Little D.P., Chorush R.A., Spier J.P., Senko M.W., Kelleher N.L., and McLafferty F.W. Rapid Sequencing of Oligonucleotides by High-Resolution Mass Spectrometry. J. Am. Chem. Soc 116 (1994) 4893-4897
38. Ni J., Pomerantz C., Rozenski J., Zhang Y., and McCloskey J.A. Interpretation of Oligonucleotide Mass Spectra for Determination of Sequence Using Electrospray Ionization and Tandem Mass Spectrometry. Anal. Chem 68 13 (1996) 1989-1999
39. Fitzgerald M.C., Zhu L., and Smith L.M. The Analysis of Mock DNA-Sequencing Reactions Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Rapid Commun. Mass Spectrom 7 (1993) 895-897
40. Shaler T.A., Tan Y., Wickham J.N., Wu K.J., and Becker C.H. Analysis of Enzymatic DNA Sequencing Reactions by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Rapid Commun. Mass Spectrom 9 (1995) 1172-1176
41. Koster H., Tang K., Fu D.J., Braun A., van den Boom D., Smith C.L., Cotter R.J., and Cantor C.R. A Strategy for Rapid and Efficient DNA Sequencing by Mass Spectrometry. Nat. Biotechnol 14 9 (1996) 1123-1128
42. Pieles U., Zurcher W., Schar M., and Moser H.E. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry: A Powerful Tool for the Mass and Sequence Analysis of Natural and Modified Oligonucleotides. Nucleic Acids Res 21 14 (1993) 3191-3196
43. Limbach P.A., McCloskey J.A., and Crain P.F. Enzymatic Sequencing of Oligonucleotides with Electrospray Mass Spectrometry. Nucleic Acids Res. Symp. Ser 31 (1994) 127-128
44. Bentzley C.M., Johnston M.V., Larsen B.S., and Gutteridge S. Oligonucleotide Sequence and Composition Determined by Matrix-Assisted Laser Desorption/Ionization. Anal. Chem 68 13 (1996) 2141-2146
45. Smith L.M. The Future of DNA Sequencing. Science 262 5133 (1993) 530-532
46. Murray K.K. DNA Sequencing by Mass Spectrometry. J. Mass Spectrom 31 11 (1996) 1203-1215
47. Limbach P.A. Indirect Mass Spectrometric Methods for Characterizing and Sequencing Oligonucleotides. Mass Spectrom. Rev 15 (1996) 297-336
48. Swerdlow H., and Gesteland R. Capillary Gel Electrophoresis for Rapid, High Resolution DNA Sequencing. Nucleic Acids Res 18 6 (1990) 1415-1419
49. Luckey J.A., Drossman H., Kostichka A.J., Mead D.A., D'Cunha J., Norris T.B., and Smith L.M. High Speed DNA Sequencing by Capillary Electrophoresis. Nucleic Acids Res 18 15 (1990) 4417-4421
50. Hunkapiller T., Kaiser R.J., Koop B.F., and Hood L. Large-Scale and Automated DNA Sequence Determination. Science 254 5028 (1991) 59-67
51. Venter J.C., Smith H.O., and Hood L. A New Strategy for Genome Sequencing. Nature 381 6581 (1996) 364-366
52. Henry C. Can MS Really Compete in the DNA World?. Anal. Chem 69 (1997) 243A-246A
53. Little D.P., Braun A., Darnhofer-Demar B., and Koster H. Identification of Apolipoprotein E Polymorphisms Using Temperature Cycled Primer Oligo Base Extension and Mass Spectrometry. Eur. J. Clin. Chem. Clin. Biochem 35 7 (1997) 545-548
54. Haff L.A., and Smirnov I.P. Single-Nucleotide Polymorphism Identification Assays Using a Thermostable DNA Polymerase and Delayed Extraction MALDI-TOF Mass Spectrometry. Genome Res 7 4 (1997) 378-388
55. Tost J., and Gut I.G. Genotyping Single Nucleotide Polymorphisms by Mass Spectrometry. Mass Spectrom Rev 21 6 (2002) 388-418
56. Hofstadler S.A., Sampath R., Blyn L.B., Eshoo M.W., Hall T.A., Jiang Y., Drader J.J., Hannis J.C., Sannes-Lowery K.A., Cummins L.B., Libby B., Walcott D.J., Schink A., Massire C., Ranken R., Gutierrez J., Manalili S., Ivy C., Melton R.E., Levene H.M., Barrett-Wilt G., Li F., Zapp V., White N., Samant V., McNeil J.A., Knize D.J., Robbins D.W., Rudnick K., Desai A., Moradi E., and Ecker D. TIGER: The Universal Biosensor. Int. J. Mass Spectrom 242 (2005) 23-41
57. Ecker D.J., Sampath R., Blyn L.B., Eshoo M.W., Ivy C., Ecker J.A., Libby B., Samant V., Sannes-Lowery K.A., Melton R.E., Russell K., Freed N., Barrozo C., Wu J., Rudnick K., Desai A., Moradi E., Knize D.J., Robbins D.W., Hannis J.C., Harrell P.M., Massire C., Hall T.A., Jiang Y., Ranken R., Drader J.J., White N., McNeil J.A., Crooke S.T., and Hofstadler S.A. Rapid Identification and Strain-Typing of Respiratory Pathogens for Epidemic Surveillance. Proc. Natl. Acad. Sci. U.S.A 102 22 (2005) 8012-8017
58. Sampath R., Hall T.A., Massire C., Li F., Blyn L.B., Eshoo M.W., Hofstadler S.A., and Ecker D.J. Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry. Ann. N.Y. Acad. Sci 1102 (2007) 109-120
59. Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., and Watanabe C. Identifying Proteins from Two-Dimensional Gels by Molecular Mass Searching of Peptide Fragments in Protein Sequence Databases. Proc. Natl. Acad. Sci. U.S.A 90 (1993) 5011-5015
60. Shevchenko A., Jensen O.N., Podtelejnikov A.V., Sagliocco F., Wilm M., Vorm O., Mortensen P., Shevchenko A., Boucherie H., and Mann M. Linking Genome and Proteome by Mass Spectrometry: Large-Scale Identification of Yeast Proteins from Two-Dimensional Gels. Proc. Natl. Acad. Sci. U.S.A 93 25 (1996) 14440-14445
61. Aebersold R., and Mann M. Mass-Spectrometry-Based Proteomics. Nature 422 (2003) 198-207
62. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., Doucette-Stamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Raymond C., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., and Chen Y.J. Initial Sequencing and Analysis of the Human Genome. Nature 409 6822 (2001) 860-921
63. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C., Yao A., Ye J., Zhan M., Zhang W., Zhang H., Zhao Q., Zheng L., Zhong F., Zhong W., Zhu S., Zhao S., Gilbert D., Baumhueter S., Spier G., Carter C., Cravchik A., Woodage T., Ali F., An H., Awe A., Baldwin D., Baden H., Barnstead M., Barrow I., Beeson K., Busam D., Carver A., Center A., Cheng M.L., Curry L., Danaher S., Davenport L., Desilets R., Dietz S., Dodson K., Doup L., Ferriera S., Garg N., Gluecksmann A., Hart B., Haynes J., Haynes C., Heiner C., Hladun S., Hostin D., Houck J., Howland T., Ibegwam C., Johnson J., Kalush F., Kline L., Koduru S., Love A., Mann F., May D., McCawley S., McIntosh T., McMullen I., Moy M., Moy L., Murphy B., Nelson K., Pfannkoch C., Pratts E., Puri V., Qureshi H., Reardon M., Rodriguez R., Rogers Y.H., Romblad D., Ruhfel B., Scott R., Sitter C., Smallwood M., Stewart E., Strong R., Suh E., Thomas R., Tint N.N., Tse S., Vech C., Wang G., Wetter J., Williams S., Williams M., Windsor S., Winn-Deen E., Wolfe K., Zaveri J., Zaveri K., Abril J.F., Guigo R., Campbell M.J., Sjolander K.V., Karlak B., Kejariwal A., Mi H., Lazareva B., Hatton T., Narechania A., Diemer K., Muruganujan A., Guo N., Sato S., Bafna V., Istrail S., Lippert R., Schwartz R., Walenz B., Yooseph S., Allen D., Basu A., Baxendale J., Blick L., Caminha M., Carnes-Stine J., Caulk P., Chiang Y.H., Coyne M., Dahlke C., Mays A., Dombroski M., Donnelly M., Ely D., Esparham S., Fosler C., Gire H., Glanowski S., Glasser K., Glodek A., Gorokhov M., Graham K., Gropman B., Harris M., Heil J., Henderson S., Hoover J., Jennings D., Jordan C., Jordan J., Kasha J., Kagan L., Kraft C., Levitsky A., Lewis M., Liu X., Lopez J., Ma D., Majoros W., McDaniel J., Murphy S., Newman M., Nguyen T., Nguyen N., Nodell M., Pan S., Peck J., Peterson M., Rowe W., Sanders R., Scott J., Simpson M., Smith T., Sprague A., Stockwell T., Turner R., Venter E., Wang M., Wen M., Wu D., Wu M., Xia A., Zandieh A., and Zhu X. The Sequence of the Human Genome. Science 291 5507 (2001) 1304-1351
64. Consortium I.H.G.S. Finishing the Euchromatic Sequence of the Human Genome. Nature 431 7011 (2004) 931-945
65. Pheasant M., and Mattick J.S. Raising the Estimate of Functional Human Sequences. Genome Res 17 9 (2007) 1245-1253
66. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E., Kuehn M.S., Taylor C.M., Neph S., Koch C.M., Asthana S., Malhotra A., Adzhubei I., Greenbaum J.A., Andrews R.M., Flicek P., Boyle P.J., Cao H., Carter N.P., Clelland G.K., Davis S., Day N., Dhami P., Dillon S.C., Dorschner M.O., Fiegler H., Giresi P.G., Goldy J., Hawrylycz M., Haydock A., Humbert R., James K.D., Johnson B.E., Johnson E.M., Frum T.T., Rosenzweig E.R., Karnani N., Lee K., Lefebvre G.C., Navas P.A., Neri F., Parker S.C., Sabo P.J., Sandstrom R., Shafer A., Vetrie D., Weaver M., Wilcox S., Yu M., Collins F.S., Dekker J., Lieb J.D., Tullius T.D., Crawford G.E., Sunyaev S., Noble W.S., Dunham I., Denoeud F., Reymond A., Kapranov P., Rozowsky J., Zheng D., Castelo R., Frankish A., Harrow J., Ghosh S., Sandelin A., Hofacker I.L., Baertsch R., Keefe D., Dike S., Cheng J., Hirsch H.A., Sekinger E.A., Lagarde J., Abril J.F., Shahab A., Flamm C., Fried C., Hackermuller J., Hertel J., Lindemeyer M., Missal K., Tanzer A., Washietl S., Korbel J., Emanuelsson O., Pedersen J.S., Holroyd N., Taylor R., Swarbreck D., Matthews N., Dickson M.C., Thomas D.J., Weirauch M.T., Gilbert J., Drenkow J., Bell I., Zhao X., Srinivasan K.G., Sung W.K., Ooi H.S., Chiu K.P., Foissac S., Alioto T., Brent M., Pachter L., Tress M.L., Valencia A., Choo S.W., Choo C.Y., Ucla C., Manzano C., Wyss C., Cheung E., Clark T.G., Brown J.B., Ganesh M., Patel S., Tammana H., Chrast J., Henrichsen C.N., Kai C., Kawai J., Nagalakshmi U., Wu J., Lian Z., Lian J., Newburger P., Zhang X., Bickel P., Mattick J.S., Carninci P., Hayashizaki Y., Weissman S., Hubbard T., Myers R.M., Rogers J., Stadler P.F., Lowe T.M., Wei C.L., Ruan Y., Struhl K., Gerstein M., Antonarakis S.E., Fu Y., Green E.D., Karaoz U., Siepel A., Taylor J., Liefer L.A., Wetterstrand K.A., Good P.J., Feingold E.A., Guyer M.S., Cooper G.M., Asimenos G., Dewey C.N., Hou M., Nikolaev S., Montoya-Burgos J.I., Loytynoja A., Whelan S., Pardi F., Massingham T., Huang H., Zhang N.R., Holmes I., Mullikin J.C., Ureta-Vidal A., Paten B., Seringhaus M., Church D., Rosenbloom K., Kent W.J., Stone E.A., Batzoglou S., Goldman N., Hardison R.C., Haussler D., Miller W., Sidow A., Trinklein N.D., Zhang Z.D., Barrera L., Stuart R., King D.C., Ameur A., Enroth S., Bieda M.C., Kim J., Bhinge A.A., Jiang N., Liu J., Yao F., Vega V.B., Lee C.W., Ng P., Shahab A., Yang A., Moqtaderi Z., Zhu Z., Xu X., Squazzo S., Oberley M.J., Inman D., Singer M.A., Richmond T.A., Munn K.J., Rada-Iglesias A., Wallerman O., Komorowski J., Fowler J.C., Couttet P., Bruce A.W., Dovey O.M., Ellis P.D., Langford C.F., Nix D.A., Euskirchen G., Hartman S., Urban A.E., Kraus P., Van Calcar S., Heintzman N., Kim T.H., Wang K., Qu C., Hon G., Luna R., Glass C.K., Rosenfeld M.G., Aldred S.F., Cooper S.J., Halees A., Lin J.M., Shulha H.P., Zhang X., Xu M., Haidar J.N., Yu Y., Ruan Y., Iyer V.R., Green R.D., Wadelius C., Farnham P.J., Ren B., Harte R.A., Hinrichs A.S., Trumbower H., Clawson H., Hillman-Jackson J., Zweig A.S., Smith K., Thakkapallayil A., Barber G., Kuhn R.M., Karolchik D., Armengol L., Bird C.P., de Bakker P.I., Kern A.D., Lopez-Bigas N., Martin J.D., Stranger B.E., Woodroffe A., Davydov E., Dimas A., Eyras E., Hallgrimsdottir I.B., Huppert J., Zody M.C., Abecasis G.R., Estivill X., Bouffard G.G., Guan X., Hansen N.F., Idol J.R., Maduro V.V., Maskeri B., McDowell J.C., Park M., Thomas P.J., Young A.C., Blakesley R.W., Muzny D.M., Sodergren E., Wheeler D.A., Worley K.C., Jiang H., Weinstock G.M., Gibbs R.A., Graves T., Fulton R., Mardis E.R., Wilson R.K., Clamp M., Cuff J., Gnerre S., Jaffe D.B., Chang J.L., Lindblad-Toh K., Lander E.S., Koriabine M., Nefedov M., Osoegawa K., Yoshinaga Y., Zhu B., and de Jong P.J. Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project. Nature 447 7146 (2007) 799-816
67. Orgel L.E., and Crick F.H. Selfish DNA: The Ultimate Parasite. Nature 284 5757 (1980) 604-607
68. Doolittle W.F., and Sapienza C. Selfish Genes, the Phenotype Paradigm and Genome Evolution. Nature 284 5757 (1980) 601-603
69. Volff J.N. Turning Junk Into Gold: Domestication of Transposable Elements and the Creation of New Genes in Eukaryotes. BioEssays 28 9 (2006) 913-922
70. Mattick J.S., and Makunin I.V. Noncoding RNA. Hum. Mol. Genet 15 Spec No 1 (2006) R17-R29
71. Zuckerkandl E., and Cavalli G. Combinatorial Epigenetics, "Junk DNA," and the Evolution of Complex Organisms. Gene 390 1/2 (2007) 232-242
72. Claverie J.M. Fewer Genes, More Noncoding RNA. Science 309 5740 (2005) 1529-1530
73. Lee R.C., Feinbaum R.L., and Ambros V. The C. elegans Heterochronic Gene lin-4 Encodes Small RNAs with Antisense Complementarity to lin-14. Cell 75 5 (1993) 843-854
74. Wightman B., Ha I., and Ruvkun G. Post-Transcriptional Regulation of the Heterochronic Gene lin-14 by lin-4 Mediates Temporal Pattern Formation in C. elegans. Cell 75 5 (1993) 855-862
75. Bartel D.P. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 116 2 (2004) 281-297
76. Vasudevan S., Tong Y., and Steitz J.A. Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation. Science 318 5858 (2007) 1931-1934
77. Winkler W., Nahvi A., and Breaker R.R. Thiamine Derivatives Bind Messenger RNAs Directly to Regulate Bacterial Gene Expression. Nature 419 6910 (2002) 952-956
78. Nudler E., and Mironov A.S. The Riboswitch Control of Bacterial Metabolism. Trends Biochem. Sci 29 1 (2004) 11-17
79. Nahvi A., Sudarsan N., Ebert M.S., Zou X., Brown K.L., and Breaker R.R. Genetic Control by a Metabolite Binding mRNA. Chem. Biol 9 9 (2002) 1043-1049
80. Edwards T.E., Klein D.J., and Ferre-D'Amare A.R. Riboswitches: Small-Molecule Recognition by Gene Regulatory RNAs. Curr. Opin. Struct. Biol 17 3 (2007) 273-279
81. Hossain M., and Limbach P.A. Mass Spectrometry-Based Detection of Transfer RNAs by Their Signature Endonuclease Digestion Products. RNA 13 2 (2007) 295-303
82. Hossain M., and Limbach P.A. Multiple Endonucleases Improve MALDI-MS Signature Digestion Product Detection of Bacterial Transfer RNAs. Anal. Bioanal. Chem 394 4 (2009) 1125-1135
83. Meng Z., and Limbach P.A. Quantitation of Ribonucleic Acids Using 18O Labeling and Mass Spectrometry. Anal. Chem 77 6 (2005) 1891-1895
84. Huttenhofer A., and Vogel J. Experimental Approaches to Identify Noncoding RNAs. Nucleic Acids Res 34 2 (2006) 635-646
85. Marioni J.C., Mason C.E., Mane S.M., Stephens M., and Gilad Y. RNA-seq: An Assessment of Technical Reproducibility and Comparison with Gene Expression Arrays. Genome Res 18 9 (2008) 1509-1517
86. Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luhrmann R., and Mann M. Identification of the Proteins of the Yeast U1 Small Nuclear Ribonucleoprotein Complex by Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 94 2 (1997) 385-390
87. Kumar R., Reynolds D.M., Shevchenko A., Shevchenko A., Goldstone S.D., and Dalton S. Forkhead Transcription Factors, Fkh1p and Fkh2p, Collaborate with Mcm1p to Control Transcription Required for M-Phase. Curr. Biol 10 15 (2000) 896-906
88. Rusconi F., Guillonneau F., and Praseuth D. Contributions of Mass Spectrometry in the Study of Nucleic Acid-Binding Proteins and of Nucleic Acid-Protein Interactions. Mass Spectrom. Rev 21 (2002) 305-348
89. Steen H., and Jensen O.N. Analysis of Protein-Nucleic Acid Interactions by Photochemical Cross-Linking and Mass Spectrometry. Mass Spectrom. Rev 21 3 (2002) 163-182
90. Forde C.E., and McCutchen-Maloney S.L. Characterization of Transcription Factors by Mass Spectrometry and the Role of SELDI-MS. Mass Spectrom. Rev 21 6 (2002) 419-439
91. Smith C.A., O'Maille G., Want E.J., Qin C., Trauger S.A., Brandon T.R., Custodio D.E., Abagyan R., and Siuzdak G. METLIN: A Metabolite Mass Spectral Database. Ther. Drug Monit 27 6 (2005) 747-751
92. Kopka J., Schauer N., Krueger S., Birkemeyer C., Usadel B., Bergmuller E., Dormann P., Weckwerth W., Gibon Y., Stitt M., Willmitzer L., Fernie A.R., and Steinhauser D. The Golm Metabolome Database. Bioinformatics 21 8 (2005) 1635-1638
93. Markley J.L., Anderson M.E., Cui Q., Eghbalnia H.R., Lewis I.A., Hegeman A.D., Li J., Schulte C.F., Sussman M.R., Westler W.M., Ulrich E.L., and Zolnai Z. New Bioinformatics Resources for Metabolomics. Pac. Symp. Biocomput 12 (2007) 157-168
94. Wishart D.S., Tzur D., Knox C., Eisner R., Guo A.C., Young N., Cheng D., Jewell K., Arndt D., Sawhney S., Fung C., Nikolai L., Lewis M., Coutouly M.A., Forsythe I., Tang P., Shrivastava S., Jeroncic K., Stothard P., Amegbey G., Block D., Hau D.D., Wagner J., Miniaci J., Clements M., Gebremedhin M., Guo N., Zhang Y., Duggan G.E., Macinnis G.D., Weljie A.M., Dowlatabadi R., Bamforth F., Clive D., Greiner R., Li L., Marrie T., Sykes B.D., Vogel H.J., and Querengesser L. HMDB: The Human Metabolome Database. Nucleic Acids Res 35 (2007) D521-D526
95. Ganem B., Li Y.-T., and Henion J.D. Detection of Oligonucleotide Duplex Forms by Ion-Spray Mass Spectrometry. Tetrahedron Lett 34 (1993) 1445-1448
96. Light-Wahl K.J., Springer D.L., Winger B.E., Edmonds II C.G., Thrall B.D., and Smith R.D. Observation of a Small Oligonucleotide Duplex by Electrospray Ionization Mass Spectrometry. J. Am. Chem. Soc 115 (1993) 803-804
97. Doktycz M.J., Habibi-Goudarzi S., and McLuckey S.A. Accumulation and Storage of Ionized Duplex DNA Molecules in a Quadrupole Ion Trap. Anal. Chem 66 20 (1994) 3416-3422
98. Lecchi P., Le H.M., and Pannell L.K. 6-Aza-2-Thiothymine: A Matrix for MALDI Spectra of Oligonucleotides. Nucleic Acids Res 23 7 (1995) 1276-1277
99. Lecchi P., and Pannell L.K. The Detection of Intact Double-Stranded DNA by MALDI. Am. Soc. Mass Spectrom 6 (1995) 972-975
100. Kirpekar F., Berkenkamp S., and Hillenkamp F. Detection of Double-Stranded DNA by IR- and UV-MALDI Mass Spectrometry. Anal. Chem 71 13 (1999) 2334-2339
101. Distler A.M., and Allison J. Additives for the Stabilization of Double-Stranded DNA in UV-MALDI MS. J. Am. Soc. Mass Spectrom 13 9 (2002) 1129-1137
102. Loo J.A. Studying Noncovalent Protein Complexes by Electrospray Ionization Mass Spectrometry. Mass Spectrom. Rev 16 (1997) 1-23
103. Beck J.L., Colgrave M.L., Ralph S.F., and Sheil M.M. Electrospray Ionization Mass Spectrometry of Oligonucleotide Complexes with Drugs, Metals, and Proteins. Mass Spectrom. Rev 20 (2001) 61-87
104. Hofstadler S.A., and Griffey R.H. Analysis of Noncovalent Complexes of DNA and RNA by Mass Spectrometry. Chem. Rev 101 2 (2001) 377-390
105. Hanson C.L., and Robinson C.V. Protein-Nucleic Acid Interactions and the Expanding Role of Mass Spectrometry. J. Biol. Chem 279 24 (2004) 24907-24910
106. Goodlett D.R., Camp II D.G., Hardin C.C., Corregan M., and Smith R.D. Direct Observation of a DNA Quadruplex by Electrospray Ionization Mass Spectrometry. Rapid Commun. Mass Spectrom 22 (1993) 181-183
107. Bayer E., Bauer T., Schmeer K., Bleicher K., Maier M., and Gaus H.J. Analysis of Double-Stranded Oligonucleotides by Electrospray Mass Spectrometry. Anal. Chem 66 22 (1994) 3858-3863
108. Wunschel D.S., Fox K.F., Fox A., Bruce J.E., Muddiman D.C., and Smith R.D. Analysis of Double-Stranded Polymerase Chain Reaction Products from the Bacillus cereus Group by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom 10 1 (1996) 29-35
109. Rodrigues Hoyne P., Benson L.M., Veenstra T.D., Maher III L.J., and Naylor S. RNA-RNA Noncovalent Interactions Investigated by Microspray Ionization Mass Spectrometry. Rapid Commun. Mass Spectrom 15 17 (2001) 1539-1547
110. David W.M., Brodbelt J.S., Kerwin S.M., and Thomas P.W. Investigation of Quadruplex Oligonucleotide-Drug interaction by Electrospray Ionization Mass Spectrometry. Anal. Chem 74 (2002) 2029-2033
111. Cheng X., Harms A.C., Goudreau P.N., Terwilliger T.C., and Smith R.D. Direct Measurement of Oligonucleotide Binding Stoichiometry of Gene V Protein by Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A 93 14 (1996) 7022-7027
112. Cheng X., Morin P.E., Harms A.C., Bruce J.E., Ben-David Y., and Smith R.D. Mass Spectrometric Characterization of Sequence-Specific Complexes of DNA and Transcription Factor PU 1 DNA Binding Domain. Anal. Biochem 239 (1996) 35-40
113. Sannes-Lowery K.A., Hu P., Mack D.P., Mei H.Y., and Loo J.A. HIV-1 Tat Peptide Binding to TAR RNA by Electrospray Ionization Mass Spectrometry. Anal. Chem 69 24 (1997) 5130-5135
114. Potier N., Donald L.J., Chernushevich I., Ayed A., Ens W., Arrowsmith C.H., Standing K., and Duckworth H.W. Study of a Noncovalent TRP Repressor-DNA Operator Complex by Electrospray Ionization Time-of-Flight Mass Spectrometry. Protein Sci 7 6 (1998) 1388-1395
115. Craig T.A., Benson L.M., Tomlinson A.J., Veenstra T.D., Naylor S., and Kumar R. Analysis of Transcription Complexes and Effects of Ligands by Microspray Ionization Mass Spectrometry. Nat. Biotechnol 17 12 (1999) 1214-1218
116. Deterding L.J., Kast J., Przybylski M., and Tomer K.B. Molecular Characterization of a Tetramolecular Complex Between dsDNA and a DNA-Binding Leucine Zipper Peptide Dimer by Mass Spectrometry. Bioconj. Chem 11 3 (2000) 335-344
117. Hsieh Y.L., Li Y.T., Henion J.D., and Ganem B. Studies of Noncovalent Interactions of Actinomycin D with Single-Stranded Oligodeoxynucleotides by Ion Spray Mass Spectrometry and Tandem Mass Spectrometry. Biol. Mass Spectrom 23 5 (1994) 272-276
118. Gale D.C., Goodlett D..R., Light-Wahl K.J., and Smith R.D. Observation of Duplex DNA-Drug Noncovalent Complexes by Electrospray Mass Spectrometry. J. Am. Chem. Soc 116 (1994) 6027-6028
119. Triolo A., Arcamone F.M., Raffaelli A., and Salvadori P. Noncovalent Complexes Between DNA-Binding Drugs and Double-Stranded Deoxynucleotides: A Study by Ion Spray Mass Spectrometry. J. Mass Spectrom 32 (1997) 1186-1194
120. Gupta R., Kapur A., Beck J.L., and Sheil M.M. Positive Ion Electrospray Ionization Mass Spectrometry of Double-Stranded DNA/Drug Complexes. Rapid Commun. Mass Spectrom 15 24 (2001) 2472-2480
121. Greig M., Gaus H., Cummins L.L., Sasmor H., and Griffey R.H. Measurement of Macromolecular Binding Using Electrospray Mass Spectrometry. Determination of Dissociation Constants for Oligonucleotide-Serum Albumin Complexes. J. Am. Chem. Soc 117 (1995) 10765-10766
122. Kapur A., Beck J.L., Brown S.E., Dixon N.E., and Sheil M.M. Use of Electrospray Mass Spectrometry to Study the Binding Interactions Between a Replication Terminator Protein and DNA. Protein Sci 11 1 (2002) 147-157
123. Griffey R.H., Hofstadler S.A., Sannes-Lowery K.A., Ecker D.J., and Crooke S.T. Determinants of Aminoglycoside-Binding Specificity for rRNA by Using Mass Spectrometry. Proc. Nat. Acad. Sci. U.S.A 96 18 (1999) 10129-10133
124. Wan K.X., Shibue T., and Gross M.L. Noncovalent Complexes Between DNA-Binding Drugs and Double-Stranded Oligodeoxynucleotides: A Study by ESI Ion-Trap Mass Spectrometry. J. Am. Chem. Soc 122 (2000) 300-307
125. Sannes-Lowery K.A., Griffey R.H., and Hofstadler S.A. Measuring Dissociation Constants of RNA and Aminoglycoside Antibiotics by Electrospray Ionization Mass Spectrometry. Anal. Biochem 280 2 (2000) 264-271
126. Rosu F., Gabelica V., Houssier C., and De Pauw E. Determination of Affinity, Stoichiometry, and Sequence Selectivity of Minor Groove Binder Complexes with Double-Stranded Oligodeoxynucleotides by Electrospray Ionization Mass Spectrometry. Nucleic Acids Res 30 16 (2002) e82
127. Hagan N., and Fabris D. Direct Mass Spectrometric Determination of the Stoichiometry and Binding Affinity of the Complexes Between HIV-1 Nucleocapsid Protein and RNA Stem-Loops Hairpins of the HIV-1 Ψ-Recognition Element. Biochemistry 42 36 (2003) 10736-10745
128. Gooding K.B., Higgs R., Hodge B., Stauffer E., Heinz B., McKnight K., Phipps K., Shapiro M., Winkler M., Ng W.L., and Julian R.K. High Throughput Screening of Library Compounds Against an Oligonucleotide Substructure of an RNA Target. J. Am. Soc. Mass Spectrom 15 6 (2004) 884-892
129. Daniel J.M., Friess S.D., Rajagopalan S., Wendt S., and Zenobi R. Quantitative Determination of Noncovalent Binding Interactions Using Soft Ionization Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes 216 (2002) 1-27
130. Mei H.Y., Mack D., Galan A.A., Halim N.S., Heldsinger A., Loo J.A., Moreland D.W., Sannes-Lowery K.A., Sharmeen L., Truong H.N., and Czarnik A.W. Discovery of Selective, Small-Molecule Inhibitors of RNA Complexes. I. The Tat Protein/TAR RNA Complexes Required for HIV-1 Transcription. Bioorg. Med. Chem 5 6 (1997) 1173-1184
131. Gabelica V., De Pauw E., and Rosu F. Interaction Between Antitumor Drugs and a Double-Stranded Oligonucleotide Studied by Electrospray Ionization Mass Spectrometry. J. Mass Spectrom 34 12 (1999) 1328-1337
132. Sannes-Lowery K.A., Mei H.-Y., and Loo J.A. Studying Aminoglycoside Antibiotic Binding to HIV-1 TAR RNA by Electrospray Ionization Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes 193 (1999) 115-122
133. Hofstadler S.A., Sannes-Lowery K.A., Crooke S.T., Ecker D.J., Sasmor H., Manalili S., and Griffey R.H. Multiplexed Screening of Neutral Mass-Tagged RNA Targets Against Ligand Libraries with Electrospray Ionization FTICR MS: A Paradigm for High-Throughput Affinity Screening. Anal. Chem 7 16 (1999) 3436-3440
134. Turner K.B., Brinson R.G., Yi-Brunozzi H.Y., Rausch J.W., Miller J.T., Le Grice S.F.J., Marino J.P., and Fabris D. Structural Probing of HIV-1 Polypurine Tract RNA:DNA Hybrid Using Classic Nucleic Acid Ligands. Nucleic Acids Res 36 (2008) 2799-2810
135. Turner K.B., Hagan N.A., and Fabris D. Inhibitory Effects of Archetypical Nucleic Acid Ligands on the Interactions of HIV-1 Nucleocapsid Protein with Elements of Ψ-RNA. Nucl. Acids Res 34 5 (2006) 1305-1316
136. Gale D.C., and Smith R.D. Characterization of Noncovalent Complexes Formed Between Minor Groove Binding Molecules and Duplex DNA by Electrospray Ionization-Mass Spectrometry. J. Am. Soc. Mass Spectrom 6 (1995) 1154-1164
137. Kapur A., Beck J.L., and Sheil M.M. Observation of Daunomycin and Nogalamycin Complexes with Duplex DNA Using Electrospray Ionization Mass Spectrometry. Rapid Commun. Mass Spectrom 13 (1999) 2489-2497
138. Rostom A.A., Fucini P., Benjamin D.R., Juenemann R., Nierhaus K.H., Hartl F.U., Dobson C.M., and Robinson C.V. Detection and Selective Dissociation of Intact Ribosomes in a Mass Spectrometer. Proc. Nat. Acad. Sci. U.S.A 97 10 (2000) 5185-5190
139. Liu C., Pasa-Tolic L., Hofstadler S.A., Harms A.C., Smith R.D., Kang C., and Sinha N. Probing RegA/RNA Interactions Using Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry. Anal. Biochem 262 1 (1998) 67-76
140. Reyzer M.L., Brodbelt J.S., Kerwin S.M., and Kumar D. Evaluation of Complexation of Metal-Mediated DNA-Binding Drugs to Oligonucleotides Via Electrospray Ionization Mass Spectrometry. Nucleic Acids Res 29 21 (2001) e103
141. Rosu F., Gabelica V., Houssier C., Colson P., and De Pauw E. Triplex and Quadruplex DNA Structures Studied by Electrospray Mass Spectrometry. Rapid Commun. Mass Spectrom 16 18 (2002) 1729-1736
142. Wan K.X., Gross M.L., and Shibue T. Gas-Phase Stability of Double-Stranded Oligodeoxynucleotides and Their Noncovalent Complexes with DNA-Binding Drugs as Revealed by Collisional Activation in an Ion Trap. J. Am. Soc. Mass Spectrom 11 5 (2000) 450-457
143. Gabelica V., Rosu F., Houssier C., and De Pauw E. Gas Phase Thermal Denaturation of an Oligonucleotide Duplex and Its Complexes with Minor Groove Binders. Rapid Commun. Mass Spectrom 14 6 (2000) 464-467
144. Gabelica V., and De Pauw E. Comparison of the Collision-Induced Dissociation of Duplex DNA at Different Collision Regimes: Evidence for a Multistep Dissociation Mechanism. J. Am. Soc. Mass Spectrom 13 1 (2002) 91-98
145. Gabelica V., and De Pauw E. Comparison Between Solution-Phase Stability and Gas-Phase Kinetic Stability of Oligodeoxynucleotide Duplexes. J. Mass Spectrom 36 4 (2001) 397-402
146. Schnier P.D., Klassen J.S., Strittmatter E.F., and Williams E.R. Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson-Crick Base Pairing in Vacuo. J. Am. Chem. Soc 120 37 (1998) 9605-9613
147. Mazzitelli C.L., Brodbelt J.S., Kern J.T., Rodriguez M., and Kerwin S.M. Evaluation of Binding of Perylene Diimide and Benzannulated Perylene Diimide Ligands to DNA by Electrospray Mass Spectrometry. J. Am. Soc. Mass Spectrom 17 (2006) 593-604
148. Yu E., and Fabris D. Direct Probing of RNA Structures and RNA-Protein Interactions in the HIV-1 Packaging Signal by Chemical Modification and Electrospray Ionization Fourier Transform Mass Spectrometry. J. Mol. Biol 330 2 (2003) 211-223
149. Yu E.T., and Fabris D. Toward Multiplexing the Application of Solvent Accessibility Probes for the Investigation of RNA Three-Dimensional Atructures by Electrospray Ionization-Fourier Transform Mass Spectrometry. Anal. Biochem 344 (2004) 356-366
150. Kellersberger K.A., Yu E., Kruppa G.H., Young M.M., and Fabris D. Top-Down Characterization of Nucleic Acids Modified by Structural Probes Using High-Resolution Tandem Mass Spectrometry and Automated Data Interpretation. Anal. Chem 76 9 (2004) 2438-2445
151. Zhang Q., Yu E.T., Kellersberger K.A., Crosland E., and Fabris D. Toward Building a Database of Bifunctional Probes for the MS3D Investigation of Nucleic Acids Structures. J. Am. Soc. Mass Spectrom 17 (2006) 1570-1581
152. Yu E.T., Zhang Q., and Fabris D. Untying the FIV Frameshifting Pseudoknot Structure by MS3D. J. Mol. Biol 345 (2005) 69-80
153. Yu E.T., Hawkins A.E., Eaton J., and Fabris D. MS3D Structural Elucidation of the HIV-1 Packaging Signal. Proc. Natl. Acad .Sci. U.S.A 105 (2008) 12248-12253
154. Jensen O.N., Barofsky D.F., Young M.C., von Hippel P.H., Swenson S., and Seifried S.E. Direct Observation of UV-Crosslinked Protein-Nucleic Acid Complexes by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Rapid Commun. Mass Spectrom 7 6 (1993) 496-501
155. Jensen O.N., Kulkarni S., Aldrich J.V., and Barofsky D.F. Characterization of Peptide-Oligonucleotide Heteroconjugates by Mass Spectrometry. Nucleic Acids Res 24 19 (1996) 3866-3872
156. Golden M.C., Resing K.A., Collins B..D., Willis M.C., and Koch T.H. Mass Spectral Characterization of a Protein-Nucleic Acid Photocrosslink. Protein Sci 8 12 (1999) 2806-2812
157. Geyer H., Geyer R., and Pingoud V. A Novel Strategy for the Identification of Protein-DNA Contacts by Photocrosslinking and Mass Spectrometry. Nucl. Acids Res 32 (2004) e132
158. Thiede B., Urlaub H., Neubauer H., Grelle G., and Wittmann-Liebold B. Precise Determination of RNA-Protein Contact Sites in the 50 S Ribosomal Subunit of Escherichia coli. Biochem J 334 Pt. 1 (1998) 39-42
159. Urlaub H., Raker V.A., Kostka S., and Luhrmann R. Sm Protein-Sm Site RNA Interactions Within the Inner Ring of the Spliceosomal snRNP Core Structure. EMBO J 20 1/2 (2001) 187-196
160. Will C.L., Urlaub H., Achsel T., Gentzel M., Wilm M., and Luhrmann R. Characterization of Novel SF3b and 17S U2 snRNP Proteins, Including a Human Prp5p Homologue and an SF3b DEAD-Box Protein. EMBO J 21 18 (2002) 4978-4988
161. Johnston P.D., and Redfield A.G. An NMR Study of the Exchange Rates for Protons Involved in the Secondary and Tertiary Structure of Yeast tRNA Phe. Nucleic Acids Res 4 10 (1977) 3599-3615
162. Englander S.W., Sosnick T.R., Englander J.J., and Mayne L. Mechanisms and Uses of Hydrogen Exchange. Curr. Opin. Struct. Biol 6 1 (1996) 18-23
163. Ma L., and Fitzgerald M.C. A New H/D Exchange- and Mass Spectrometry-Based Method for Thermodynamic Analysis of Protein-DNA Interactions. Chem Biol 10 12 (2003) 1205-1213
164. Sperry J.B., Shi X., Rempel D.L., Nishimura Y., Akashi S., and Gross M.L. A Mass Spectrometric Approach to the Study of DNA-Binding Proteins: Interaction of Human TRF2 with Telomeric DNA. Biochemistry 47 6 (2008) 1797-1807
165. Sperry J.B., Wilcox J.M., and Gross M.L. Strong Anion Exchange for Studying Protein-DNA Interactions by H/D Exchange Mass Spectrometry. J. Am. Soc. Mass Spectrom 19 6 (2008) 887-890
166. Freitas M.A., and Marshall A.G. Gas Phase RNA and DNA Ions. 2. Conformational Dependence of the Gas-Phase H/D Exchange of Nucleotide-5′-Monophosphates. J. Am. Soc. Mass Spectrom 12 7 (2001) 780-785
167. Balbeur D., Dehareng D., and De Pauw E. Conformationally Driven Gas-Phase H/D Exchange of Dinucleotide Negative Ions. J. Am. Soc. Mass Spectrom 18 10 (2007) 1827-1834
168. Hofstadler S.A., Sannes-Lowery K.A., and Griffey R.H. Enhanced Gas-Phase Hydrogen-Deuterium Exchange of Oligonucleotide and Protein Ions Stored in an External Multipole Ion Reservoir. J. Mass Spectrom 35 1 (2000) 62-70
169. Balbeur D., Widart J., Leyh B., Cravello L., and De Pauw E. Detection of Oligonucleotide Gas-Phase Conformers: H/D Exchange and Ion Mobility as Complementary Techniques. J. Am. Soc. Mass Spectrom 19 7 (2008) 938-946
170. Mo J., Todd G.C., and Hakansson K. Characterization of Nucleic Acid Higher Order Structure by Gas-Phase H/D Exchange in a Quadrupole-FT-ICR Mass Spectrometer. Biopolymers 91 4 (2009) 256-264
171. Turner K.B., Hagan N.A., Kohlway A., and Fabris D. Mapping Noncovalent Ligand Binding to Stemloop Domains of the HIV-1 Packaging Signal by Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom 17 (2006) 1401-1411
172. Turner K.B., Kohlway A.S., Hagan N.A., and Fabris D. Noncovalent Probes for the Investigation of Structure and Dynamics of Protein-Nucleic Acid Assemblies: The Case of NC-Mediated Dimerization of Genomic RNA in HIV-1. Biopolymers 91 4 (2009) 283-296
173. Griffey R.H., Greig M.J., Haoyun A., Sasmor H., and Manalili S. Targeted Site-Specific Gas-Phase Cleavage of Oligoribonucleotides. Application in Mass Spectrometry-Based Identification of Ligand Binding Sites. J. Am. Chem. Soc 121 (1999) 474-475
174. Hanson C.L., Fucini P., Ilag L.L., Nierhaus K.H., and Robinson C.V. Dissociation of Intact Escherichia coli Ribosomes in a Mass Spectrometer-Evidence for Conformational Change in a Ribosome Elongation Factor G Complex. J. Biol. Chem 278 2 (2002) 1259-1267
175. Turner K.B., Hagan N.A., and Fabris D. Understanding the Isomerization of the HIV-1 Dimerization Initiation Domain by the Nucleocapsid Protein. J. Mol. Biol 369 (2007) 812-828
176. Baker E.S., Dupuis N.F., and Bowers M.T. DNA Hairpin, Pseudoknot, and Cruciform Stability in a Solvent-Free Environment. J. Phys. Chem. B 113 6 (2009) 1722-1727
177. Stults J.T., Marsters J.C., and Carr S.A. Improved Electrospray Ionization of Synthetic Oligodeoxynucleotides. Rapid Commun. Mass Spectrom 5 (1991) 359-363
178. Nordhoff E., Ingendoh A., Cramer R., Overberg A., Stahl B., Karas M., Hillenkamp F., and Crain P.F. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry of Nucleic Acids with Wavelengths in the Ultraviolet and Infrared. Rapid Commun. Mass Spectrom 6 12 (1992) 771-776
179. Little D.P., Thannhauser T.W., and McLafferty F.W. Verification of 50- to 100-mer DNA and RNA Sequences with High-Resolution Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A 92 6 (1995) 2318-2322
180. Limbach P.A., Crain P.F., and McCloskey J.A. Molecular Mass Measurement of Intact Ribonucleic Acids Via Electrospray Ionization Quadrupole Mass Spectrometry. J. Am. Soc. Mass Spectrom 6 (1995) 27-39
181. Muddiman D.C., Cheng X., Udseth H.R., and Smith R.D. Charge-State Reduction with Improved Signal Intensity of Oligonucleotides in Electrospray Ionization Mass Spectrometry. J. Am. Soc. Mass Spectrom 7 (1996) 697-706
182. Liu C., Wu Q., Harms A.C., and Smith R.D. On-Line Microdialysis Sample Cleanup for Electrospray Ionization Mass Spectrometry of Nucleic Acid Samples. Anal. Chem 68 18 (1996) 3295-3299
183. Xu N.Y., Lin Y., Hofstadler S.A., Matson D., Call C.J., and Smith R.D. A Microfabricated Dialysis Device for Sample Cleanup in Electrospray Ionization Mass Spectrometry. Anal. Chem 70 17 (1998) 3553-3556
184. Hannis J.C., and Muddiman D.C. Characterization of a Microdialysis Approach to Prepare Polymerase Chain Reaction Products for Electrospray Ionization Mass Spectrometry Using On-Line Ultraviolet Absorbance Measurements and Inductively Coupled Plasma Atomic Emission Spectroscopy. Rapid Commun. Mass Spectrom 13 (1999) 323-330
185. Turner K.B., Monti S., and Fabris D. Like Polarity Ion-Ion Reactions Enable the Investigation of Specific Metal Interactions in Nucleic Acids and Their Noncovalent Assemblies. J. Am. Chem. Soc 30 (2008) 13353-13363
186. Zubarev R.A., Kelleher N.L., and McLafferty F.W. Electron Capture Dissociation of Multiply Charged Protein Cations: A Nonergodic Process. J. Am. Chem. Soc 120 (1998) 3265-3266
187. Syka J.E.P., Coon J.J., Schroeder M.J., Shabanowitz J., and Hunt D.F. Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry. Proc. Nat. Acad. Sci. U.S.A 101 (2004) 9528-9533
188. Yang J., Mo J., Adamson J.T., and Hakansson K. Characterization of Oligodeoxynucleotides by Electron Detachment Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem 77 6 (2005) 1876-1882