Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of oligonucleotides

Current Protocols in Nucleic Acid Chemistry

Volumn , Issue SUPPL. 33, 2008, Pages

  Castleberry, Colette M ^a   Chou, Chau Wen ^b   Limbach, Patrick A ^a  

^a UNIVERSITY OF CINCINNATI   (United States)

^b LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

Author keywords

MALDI; MALDI TOFMS; Nucleic acids; Purification; Sequencing

Indexed keywords

2',4',6' TRIHYDROXYACETOPHENONE; 3 HYDROXYPICOLINIC ACID; 6 AZATHIOTHYMINE; ACETOPHENONE DERIVATIVE; AMMONIUM CITRATE; AMMONIUM DERIVATIVE; ANTHRANILIC ACID DERIVATIVE; ANTHRANILIC ACID( 2 AMINOBENZOIC ACID); NICOTINIC ACID; OLIGONUCLEOTIDE; PICOLINIC ACID; PICOLINIC ACID DERIVATIVE; SEPHADEX; THYMINE DERIVATIVE; UNCLASSIFIED DRUG;

ACCURACY; ANALYTIC METHOD; CALIBRATION; DNA METHYLATION; DNA PURIFICATION; GENOTYPE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PURIFICATION; REVIEW; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 57349152179     PISSN: 19349270     EISSN: 19349289     Source Type: Journal    
DOI: 10.1002/0471142700.nc1001s33     Document Type: Review

References (90)

1. Ball, R.W. and Packman, L.C. 1997. Matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry as a rapid quality control method in oligonucleotide synthesis. Anal. Biochem. 248:185-194.
2. Bentzley, C.M., Johnston, M.V., Larsen, B.S., and Gutteridge, S. 1996. Oligonucleotide sequence and composition determined by matrix-assisted laser desorption/ionization. Anal. Chem. 68:2141-2146.
3. Berkenkamp, S., Menzel, C., Karas, M., and Hillenkamp, F. 1997. Performance of infrared matrix-assisted laser desorption/ionization mass spectrometry with lasers emitting in the 3 μm wavelength range. Rapid. Commun. Mass Spectrom. 11:1399-1406.
4. Berkenkamp, S., Kirpekar, F., and Hillenkamp, F. 1998. Infrared MALDI mass spectrometry of large nucleic acids. Science 281:260-262.
5. Bleczinski, C.F. and Richert, C. 1998. Monitoring the hybridization of the components of oligonucleotide mixtures to immobilized DNA via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid. Commun. Mass Spectrom. 12:1737-1743.
6. Braun, A., Little, D.P., Reuter, D., Muller-Mysok, B., and Koster, H. 1997. Improved analysis of microsatellites using mass spectrometry. Genomics 46:18-23.
7. Brown, R.S. and Lennon, J.J. 1995. Mass resolution improvement by incorporation of pulsed ion extraction in a matrix-assisted laser desorption ionization time-of-flight mass spectrometer. Anal. Chem. 67:1998-2003.
8. Butler, J.M. and Becker, C.H. 2001. Improved analysis of DNA short tandem repeats with time-of-flight mass spectrometry. Final Report for NIJ Grant 97-LB-VX-0003, Office of Justice Programs, National Institute of Justice (75 published pages); http://www.ojp.usdoj.gov/nij/ pubs-sum/188292.htm
9. Butler, J.M., Jiang-Baucom, P., Huang, M., Belgrader, P., and Girard, J. 1996. Peptide nucleic acid characterization by MALDI-TOF mass spectrometry. Anal. Chem. 68:3283-3287.
10. Butler, J.M., Li, J., Shaler, T.A., Monforte, J.A., and Becker, C.H. 1998. Reliable genotyping of short tandem repeat loci without an allelic ladder using time-of-flight mass spectrometry. Int. J. Legal Med. 112:45-49.
11. Carey, L. and Mitnik, L. 2002. Trends in DNA forensic analysis. Electrophoresis 23:1386-1397.
12. Cheng, S.-W. and Chan, T.-W.D. 1996. Use of ammonium halides as co-matrices for matrix-assisted laser desorption/ionization studies of oligonucleotides. Rapid Commun. Mass Spectrom. 10:907-910.
13. Colby, S.M., King, T.B., and Reilly, J.P. 1994. Improving the resolution of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry by exploiting the correlation between ion position and velocity. Rapid Commun. Mass Spectrom. 8:865-868.
14. Currie, G.J. and Yates, J.R. III. 1993. Analysis of oligodeoxynucleotides by negative-ion matrix-assisted laser desorption mass spectrometry. J. Am. Soc. Mass Spectrom. 4:955-963.
15. Edwards, A., Civitello, A., Hammond, H., and Caskey, T. 1991. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet. 49:746-756.
16. Faulstich, K., Womer, K., Brill, H., and Engels, J. 1997. A sequencing method for RNA oligonucleotides based on mass spectrometry. Anal. Chem. 69:4349-4353.
17. Fei, Z.D. and Smith, L.M. 2000. Analysis of single nucleotide polymorphisms by primer extension and matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 14:950-959.
18. Flora, J.W., Null, A.P., and Muddiman, D.C. 2002. Dual-micro-ESI source for precise mass determination on a quadrupole time-of-flight mass spectrometer for genomic and proteomic applications. Anal. Bioanal. Chem. 373:538-546.
19. Griffin, T.J. and Smith, L.M. 2000. Genetic identification bymass spectrometric analysis of single-nucleotide polymorphisms: Ternary encoding of genotypes. Anal. Chem. 72:3298-3302.
20. Griffin, T.J., Hall, J.G., Prudent, J.R., and Smith, L.M. 1999. Direct genetic analysis by matrix-assisted laser desorption ionization mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 96:6301-6306.
21. Guo, B. 1999. Mass spectrometry in DNA analysis. Anal. Chem. 71:333R-337R.
22. Haff, L.A. and Smirnov, I.P. 1997a. Multiplex genotyping of PCR products with Mass Tag-labeled primers. Nucleic Acids Res. 25:3749-3750.
23. Haff, L.A. and Smirnov, I.P. 1997b. Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry. Genome Res. 7:378-388.
24. Hahner, S., Schneider, A., Ingendoh, A., and Mosner, J. 2000. Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry. Nucleic Acids Res. 28:e82.
25. Hannis, J.C. and Muddiman, D.C. 1999. Accurate characterization of the tyrosine hydroxylase forensic allele 9.3 through development of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 13:954-962.
26. Hannis, J.C. and Muddiman, D.C. 2001. Genotyping short tandem repeats using flow injection and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commmun. Mass Spectrom. 15:348-350.
27. Havlis, J. and Trbusek, M. 2002. 5-methylcytosine as a marker for the monitoring of DNA methylation. J. Chrom. B. 781:373-392.
28. Higgins, G.S., Little, D.P., and Koster, H. 1997. Competitive oligonucleotide single-base extension combined with mass spectrometric detection for mutation screening. BioTechniques 23:710-714.
29. Hurst, G.B., Weaver, K., Doktycz, M.J., Buchanan, M.V., Costello, A.M., and Lidstrom, M.E. 1998. MALDITOF analysis of polymerase chain reaction products from methanotrophic bacteria. Anal. Chem. 70:2693-2698.
30. Juhasz, P., Roskey, M.T., Smirnov, I.P., Haff, L.A., Vestal, M.L., and Martin, S.A. 1996. Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis. Anal. Chem. 68:941-946.
31. Juhasz, P., Vestal, M.L., and Martin, S.A. 1997. On the initial velocity of ions generated by matrix-assisted laser desorption ionization and its effect on the calibration of delayed extraction time-of-flight mass spectra. J. Am. Soc. Mass. Spectrom. 8:209-217.
32. Jurinke, C., Van Den Boom, D., and Koster, H. 1998a. Asymmetric polymerase chain reaction improves streptavidin-biotin based purification of polymerase chain reaction products prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. Rapid Commun. Mass Spectrom. 12:50-52.
33. Jurinke, C., Zollner, B., Feucht, H.H., Van Den Boom, D., Jacob, A., Polywka, S., Laufs, R., and Koster, H. 1998b. Application of nested PCR and mass spectrometry for DNA-based virus detection: HBV-DNA detected in the majority of isolated anti-HBc positive sera. Genet. Anal. 14:97-102.
34. Karas, M. and Hillenkamp, F. 1988. Laser desorption ionization of proteins with molecularmasses exceeding 10,000 daltons. Anal. Chem. 60:2299-2301.
35. Karas, M., Bachmann, D., Bahr, U., and Hillenkamp, F. 1987. Matrix-assisted ultraviolet laser desorption of non-volatile compounds. Int. J. Mass Spectrom. Ion Process. 78:53-68.
36. Keough, T., Baker, T.R., Dobson, R.L.M., Lacey, M.P., Riley, T.A., Hasselfield, J.A., and Hesselberth, P.E. 1993. Antisense DNA oligonucleotides II: The use of matrix-assisted laser desorption/ ionization mass spectrometry for the sequence verification of methylphosphonate oligodeoxyri bonucleotides. Rapid Commun. Mass Spectrom. 7:195-200.
37. Keough, T., Shaffer, J.D., Lacey, M.P., Riley, T.A., Marvin, W.B., Scurria, M.A., Hasselfield, J.A., and Hesselberth, E.P. 1996. Detailed characterization of antisense DNA oligonucleotides. Anal. Chem. 68:3405-3412.
38. Kim, S., Edwards, J.R., Deng, L., Chung, W., and Ju, J. 2002. Solid phase capturable dideoxynucleotides for multiplex genotyping using mass spectrometry. Nucleic Acids Res. 30:e85.
39. Knochenmuss, R. 2006. Ion formation mechanisms in UV-MALDI. Analyst 131:966-986.
40. Langley, G., Herniman, J., Davies, N., and Brown, T. 1999. Simplified sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 13:1717-1723.
41. Li, J., Butler, J.M., Tan, Y.P., Lin, H., Royer, S., Ohler, L., Shaler, T.A., Hunter, J.M., Pollart, D.J., Monforte, J.A., and Becker, C.H. 1999. Single nucleotide polymorphism determination using primer extension and time-of-flight mass spectrometry. Electrophoresis 20:1258-1265.
42. Limbach, P.A. 1996. Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides. Mass Spectrom. Rev. 15:297-336.
43. Little, D.P., Braun, A., Darnhofer-Demar, B., Frilling, A., Li, Y., McIver, J., Robert, T., and Koster, H. 1997a. Detection of RET proto-oncogene codon 634 mutations using mass spectrometry. J. Mol. Med. 75:745-750.
44. Little, D.P., Braun, A., O'Donnell, M.J., and Koster, H. 1997b. Mass spectrometry from miniaturized arrays for full comparative DNA analysis. Nat. Med. 3:1413-1416.
45. Little, D.P., Cornish, T.J., Odonnell, M.J., Braun, A., Cotter, R.J., and Koster, H. 1997c. MALDI on a chip: Analysis of arrays of low femtomole to subfemtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipet. Anal. Chem. 69:4540-4546.
46. Meng, Z. and Limbach, P.A. 2005. Quantitation of ribonucleic acids using O18 labeling and mass spectrometry. Anal. Chem. 77:1891-1895.
47. Meng, Z., Simmons-Willis, T., and Limbach, P. 2004. The use of mass spectrometry in genomics. Biomol. Eng. 21:1-13.
48. Nakai, K., Habano, W., Fujita, T., Nakai, K., Schnackenberg, J., Kawazoe, K., Suwabe, A., and Itoh, C. 2002. Highly multiplexed genotyping of coronary artery disease-associated SNPs using MALDI-TOF mass spectrometry. Hum. Mutat. 20:133-138.
49. Nordhoff, E., Kirpekar, F., and Roepstorff, P. 1996. Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 15:67-138.
50. Null, A.P. and Muddiman, D.C. 2001. Perspectives on the use of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era. J. Mass Spectrom. 36:589-606.
51. Oberacher, H., Parson, W., Muhlmann, R., and Huber, C.G. 2001. Analysis of polymerase chain reaction products by on-line liquid chromatography-mass spectrometry for genotyping of polymorphic short tandem repeat loci. Anal. Chem. 73:5109-5115.
52. Parr, G.R., Fitzgerald, M.C., and Smith, L.M. 1992. Matrix-assisted laser desorption/ionization mass spectrometry of synthetic oligodeoxyribonucleotides. Rapid Commun. Mass Spectrom. 6:369-372.
53. Pieles, U., Zürcher, W., Schär, M., and Moser, H.E. 1993. 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. 21:3191-3196.
54. Polo, L.M., McCarley, T.D., and Limbach, P.A. 1997. Chemical sequencing of phosphorothioate oligonucleotides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem. 69:1107-1112.
55. Roskey, M.T., Juhasz, P., Smirnov, I.P., Takach, E.J., Martin, S.A., and Haff, L.A. 1996. DNA sequencing by delayed extraction matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 93:4724-4729.
56. Ross, P.L. and Belgrader, P. 1997. Analysis of short tandem repeat polymorphisms in human DNA by Matrix-assisted laser desorption/ioniztion mass spectrometry. Anal. Chem. 69:3966-3972.
57. Ross, P.L., Lee, K., and Belgrader, P. 1997. Discrimination of single-nucleotide polymorphisms in human DNA using peptide nucleic acid probes detected by MALDI-TOF mass spectrometry. Anal. Chem. 69:4197-4202.
58. Ross, P., Hall, L., Smirnov, I., and Haff, L. 1998a. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16:1347-1351.
59. Ross, P.L., Davis, P.A., and Belgrader, P. 1998b. Analysis of DNA fragments from conventional and microfabricated PCR devices using delayed extraction MALDI-TOF mass spectrometry. Anal. Chem. 70:2067-2073.
60. Ross, P., Hall, L., and Haff, L.A. 2000. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 29:620-629.
61. Sarracino, D. and Richert, C. 1996. Quantitative MALDI-TOF MS of oligonucleotides and a nuclease assay. Bioorg. Med. Chem. Lett. 6:2543-2548.
62. Sauer, S. 2007. The essence of DNA sample preparation for MALDI mass spectrometry. J. Biochem. Biophys. Methods 70:311-318.
63. Sauer, S., Lechner, D., Berlin, K., Lehrach, H., Escary, J-L., Fox, N., and Gut, I.G. 2000a. A novel procedure for efficient genotyping of single nucleotide polymorphishms. Nucleic Acids Res. 28:e3.
64. Sauer, S., Lechner, D., Berlin, K., PlanCon, C., Heuermann, A., Lehrach, H., and Gut, I.G. 2000b. Full flexibility genotyping of single nucleotide polymorphishms by the GOOD assay. Nucleic Acids Res. 28:e100.
65. Sauer, S., Geelfand, D.H., Boussicault, F., Bauer, K., Reichert, F., and Gut, I.G. 2002. Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry. Nucleic Acids Res. 30:e22.
66. Schneider, K. and Chait, B.T. 1993. Matrix-assisted laser desorption mass spectrometry of homopolymer oligodeoxyribonucleotides. Influence of base composition on the mass spectrometric response. Org. Mass Spectrom. 28:1353-1361.
67. Schuette, J.M., Pieles, U., Maleknia, S.D., Srivatsa, G.S., Cole, D.L., Moser, H.E., and Afeyan, N.B. 1995. Sequence analysis of phosphorothioate oligonucleotides via matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J. Pharm. Biomed. Anal. 13:1195-1203.
68. Shaler, T.A., Tan, Y., Wickham, J.N., Wu, K.J., and Becker, C.H. 1995. Analysis of enzymatic DNA sequencing reactions by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 9:942-947.
69. Shaler, T.A., Wickham, J.N., Sannes, K.A., Wu, K.J., and Becker, C.H. 1996. Effect of impurities on the matrix-assisted laser desorption mass spectra of single-stranded oligodeoxynucleotides. Anal. Chem. 68:576-579.
70. Simmons, T.A. and Limbach, P.A. 1998. Influence of co-matrix proton affinity on oligonucleotide ion stability in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom. 9:668-675.
71. Smirnov, I.P., Roskey, M.T., Juhasz, P., Takach, E.J., Martin, S.A., and Haff, L.A. 1996. Sequencing oligonucleotides by exonuclease digestion and delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal. Biochem. 238:19-25.
72. Spengler, B. 1997. Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 32:1019-1036.
73. Spengler, B. and Bokelmann, V. 1993. Angular and time resolved intensity distributions of laser-desorbed matrix ions. Nucl. Instrum. Methods Phys. Res. B 82:379-385.
74. Srinivasan, J.R., Kachman, M.T., Killeen, A.A., Akel, N., Siemieniak, D., and Lubman, D.M. 1998. Genotyping of apolipoprotein E by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 12:1045-1050.
75. Stroman, R.C. 1994. Epigenesis: The missing beat in biotechnology. Biotechnology 12:156-163.
76. Sun, X., Ding, H., Hung, K., and Guo, B. 2000. A new MALDI-TOF based mini-sequencing assay for genotyping of SNPs. Nucleic Acids Res. 28:e68.
77. Taranenko, N.I., Golovlev, V.V., Allman, S.L., Taranenko, N.V., Chem, C.H., Hong, J., and Chang, L.Y. 1998. Matrix-assisted laser desorption/ ionization for short tandem repeat loci. Rapid Commun. Mass Spectrom. 12:413-418.
78. Tolson, D.A. and Nicholson, N.H. 1998. Sequencing RNA by a combination of exonuclease digestion and uridine specific chemical cleavage using MALDI-TOF. Nucleic Acids Res. 26:446-451.
79. Tost, J. and Gut, I.G. 2002. Genotyping single nucleotide polymorphisims by mass spectrometry. Mass Spectrom. Rev. 21:388-418.
80. Tost, J., Schatz, P., Schuster, M., Berlin, K., and Gut, I.G. 2003. Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry. Nucleic Acids Res. 31:e50.
81. van den Boom, D., Jurinke, C., Higgins, S., Becker, T., and Koster, H. 1998. Mass spectrometric DNA diagnostics. Nucleosides Nucleotides 17:2157-2164.
82. Vestal, M.L., Juhasz, P., and Martin, S.A. 1995. Delayed extraction matrix-assisted laser desorption time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 9:1044-1050.
83. Vorm, O., Roepstorff, P., and Mann, M. 1994. Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation. Anal. Chem. 66:3281-3287.
84. Wada, Y. and Yamamoto, M. 1997. Detection of single-nucleotide mutations including substitutions and deletions by matrix-assisted laser desoprtion/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 11:1657-1660.
85. Wang, D.G., Fan, J-B., Siao, C-J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., and Lander, E.S. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077-1082.
86. Werner, M., Sych, M., Herbon, N., Illig, T., Konig, I.R., and Wjst, M. 2002. Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum. Mutat. 20:57-64.
87. Worrall, T.A., Schmeckpeper, B.J., Corvera, J.S., and Cotter, R.J. 2000. Allele-specific HLA-DR typing by mass spectrometry: An alternative to hybridization-based typing methods. Anal. Chem. 72:5233-5238.
88. Wu, K.J., Steding, A., and Becker, C.H. 1993. Matrix-assisted laser desorption time-of-flight mass spectrometry of oligonucleotides using 3-hydroxypicolinic acid as an ultraviolet-sensitive matrix. Rapid Commun. Mass Spectrom. 7:142-146.
89. Zhang, L., Ren, Y., Rempel, D., Taylor, J., and Gross, M. 2001. Determination of photomodified oligodeoxynucleotides by exonuclease digestion, matrix-assisted laser desorption/ionization and post-source decay mass spectrometry. J. Am. Soc. Mass Spectrom. 12:1127-1135.
90. Zhu, Y.F., Taranenko, N.I., Allman, S.L., Martin, S.A., Haff, L., and Chen, C.H. 1996. The effect of ammonium salt and matrix in the detection of DNA by MALDI-TOF mass spectroscopy. Rapid Commun. Mass Spectrom. 10:1591-1596.