Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry of Oligonucleotides

Colette M. Castleberry1, Chau‐Wen Chou2, Patrick A. Limbach1

1 University of Cincinnati, Cincinnati, Ohio, 2 Louisiana State University Health Sciences Center, New Orleans, Louisiana
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 10.1
DOI:  10.1002/0471142700.nc1001s33
Online Posting Date:  June, 2008
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

MALDI‐MS is one of the most useful techniques available for determining biomolecule mass. It offers high mass accuracy, good sensitivity, simplicity, and speed. Because singly charged ions of oligonucleotides are typically observed, MALDI‐MS spectra are easy to interpret. This unit presents protocols for sample preparation and purification, matrix preparation, and matrix/analyte sample preparation. It provides an introduction to the instrumentation and its calibration, and a discussion of some of the useful applications of MALDI‐MS analysis in the study of oligonucleotides. This technique is typically used for 120‐mer or smaller oligonucleotides. Curr. Protoc. Nucleic Acid Chem. 33:10.1.1‐10.1.21. © 2008 by John Wiley & Sons, Inc.

Keywords: MALDI; MALDI‐TOFMS; nucleic acids; purification; sequencing

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Sample Preparation
  • Basic Protocol 1: Sample Desalting with C18 Pipet Tips
  • Alternate Protocol 1: Spin‐Column Purification of Oligonucleotides
  • Alternate Protocol 2: C18 Reversed Phase Cartridge Purification of Oligonucleotides
  • Alternate Protocol 3: Molecular‐Weight‐Cutoff‐Filter Purification of Oligonucleotides
  • MALDI Matrix and Co‐Matrix Preparation
  • Basic Protocol 2: MALDI Matrix Preparation
  • Basic Protocol 3: Ammonium Citrate MALDI Co‐Matrix Preparation
  • Matrix/Analyte Preparation for MALDI‐TOF‐MS
  • Basic Protocol 4: Matrix/Analyte Preparation
  • Alternate Protocol 4: 2′,4′,6′‐Trihydroxyacetophenone Matrix/Analyte Preparation
  • The MALDI Process and Instrumentation
  • Typical Applications of MALDI‐MS in Oligonucleotide Analysis
  • Basic Protocol 5: Sequencing Using Exonuclease Digestion and MALDI‐TOF‐MS
  • Summary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

Basic Protocol 1: Sample Desalting with C18 Pipet Tips

  Materials
  • 50% acetonitrile (HPLC grade) in autoclaved nanopure water
  • 0.1 M triethylammonium acetate (TEAA), pH 7.0
  • Oligonucleotide sample
  • Autoclaved, nanopure water
  • Fresh matrix solution (optional)
  • ZipTip C18 pipet tips (from Millipore)
  • 10‐µL pipet

Alternate Protocol 1: Spin‐Column Purification of Oligonucleotides

  Materials
  • Autoclaved, nanopure water
  • Oligonucleotide sample
  • Microspin column (e.g., Sephadex G‐25; Amersham Pharmacia Biotech, Boehringer Mannheim)
  • 1.5‐mL microcentrifuge tubes
  • Microcentrifuge, variable speed
  • Pipet

Alternate Protocol 2: C18 Reversed Phase Cartridge Purification of Oligonucleotides

  Materials
  • 50% HPLC‐grade acetonitrile in autoclaved, nanopure water
  • 2 M triethylammonium acetate (TEAA), HPLC grade
  • Oligonucleotide sample
  • Autoclaved, nanopure water
  • Oligonucleotide purification cartridge (e.g., Waters, Perkin Elmer, Glen Research)
  • 10‐mL disposable syringe

Alternate Protocol 3: Molecular‐Weight‐Cutoff‐Filter Purification of Oligonucleotides

  Materials
  • Autoclaved, nanopure water
  • Molecular‐weight‐cutoff‐filter column (e.g., Amicon, Millipore, Gelman Sciences)
  • 1.5‐mL microcentrifuge tubes
  • Microcentrifuge, variable speed

Basic Protocol 2: MALDI Matrix Preparation

  Materials
  • Matrix (Aldrich): 3‐Hydroxypicolinic acid (3‐HPA), 3‐Hydroxypicolinic acid/picolinic acid (3‐HPA/PA), or 2′, 4′, 6′‐Trihydroxyacetophenone (THAP)
  • HPLC‐grade acetonitrile or 50% HPLC‐grade acetonitrile in autoclaved, nanopure water
  • 1.5‐mL tube
  • Vortex

Basic Protocol 3: Ammonium Citrate MALDI Co‐Matrix Preparation

  Materials
  • Ammonium citrate, dibasic
  • Nanopure water
  • 15‐mL centrifuge tube

Basic Protocol 4: Matrix/Analyte Preparation

  Materials
  • Oligonucleotide sample
  • Autoclaved, nanopure water
  • Matrix solution (see protocol 5)
  • Ammonium citrate co‐matrix solution (see protocol 6)
  • 0.5‐ml tube
  • Vortex
  • Sample plate
  • Mass spectrometer

Alternate Protocol 4: 2′,4′,6′‐Trihydroxyacetophenone Matrix/Analyte Preparation

  • THAP matrix solution (see protocol 5)
  • Vortex

Basic Protocol 5: Sequencing Using Exonuclease Digestion and MALDI‐TOF‐MS

  Materials
  • Oligonucleotide sample, lyophilized
  • Autoclaved, nanopure water
  • 50% ammonium hydroxide
  • 0.1 U/µL phosphodiesterase I (snake venom, SVP; Sigma) or II (calf spleen, CSP; Worthington Biochemical) in water
  • 50 g/L ammonium citrate (dibasic), pH ∼ 6.4
  • Matrix (refer to section on Matrix Preparation to determine the appropriate matrix solutions)
  • Dry ice
  • 37°C water bath
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   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.
   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.
   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.
   Berkenkamp, S., Kirpekar, F., and Hillenkamp, F. 1998. Infrared MALDI mass spectrometry of large nucleic acids. Science 281:260‐262.
   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.
   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.
   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.
   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
   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.
   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.
   Carey, L. and Mitnik, L. 2002. Trends in DNA forensic analysis. Electrophoresis 23:1386‐1397.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   Griffin, T.J. and Smith, L.M. 2000. Genetic identification by mass spectrometric analysis of single‐nucleotide polymorphisms: Ternary encoding of genotypes. Anal. Chem. 72:3298‐3302.
   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.
   Guo, B. 1999. Mass spectrometry in DNA analysis. Anal. Chem. 71:333R‐337R.
   Haff, L.A. and Smirnov, I.P. 1997a. Multiplex genotyping of PCR products with MassTag‐labeled primers. Nucleic Acids Res. 25:3749‐3750.
   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.
   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.
   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.
   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.
   Havlis, J. and Trbusek, M. 2002. 5‐methylcytosine as a marker for the monitoring of DNA methylation. J. Chrom. B. 781:373‐392.
   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.
   Hurst, G.B., Weaver, K., Doktycz, M.J., Buchanan, M.V., Costello, A.M., and Lidstrom, M.E. 1998. MALDI‐TOF analysis of polymerase chain reaction products from methanotrophic bacteria. Anal. Chem. 70:2693‐2698.
   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.
   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.
   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.
   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.
   Karas, M. and Hillenkamp, F. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60:2299‐2301.
   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.
   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 oligodeoxyribonucleotides. Rapid Commun. Mass Spectrom. 7:195‐200.
   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.
   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.
   Knochenmuss, R. 2006. Ion formation mechanisms in UV‐MALDI. Analyst 131:966‐986.
   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.
   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.
   Limbach, P.A. 1996. Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides. Mass Spectrom. Rev. 15:297‐336.
   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.
   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.
   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.
   Meng, Z. and Limbach, P.A. 2005. Quantitation of ribonucleic acids using O18 labeling and mass spectrometry. Anal. Chem. 77:1891‐1895.
   Meng, Z., Simmons‐Willis, T., and Limbach, P. 2004. The use of mass spectrometry in genomics. Biomol. Eng. 21:1‐13.
   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.
   Nordhoff, E., Kirpekar, F., and Roepstorff, P. 1996. Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 15:67‐138.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   Ross, P., Hall, L., Smirnov, I., and Haff, L. 1998a. High level multiplex genotyping by MALDI‐TOF mass spectrometry. Nat. Biotechnol. 16:1347‐1351.
   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.
   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.
   Sarracino, D. and Richert, C. 1996. Quantitative MALDI‐TOF MS of oligonucleotides and a nuclease assay. Bioorg. Med. Chem. Lett. 6:2543‐2548.
   Sauer, S. 2007. The essence of DNA sample preparation for MALDI mass spectrometry. J. Biochem. Biophys. Methods 70:311‐318.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   Spengler, B. 1997. Post‐source decay analysis in matrix‐assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 32:1019‐1036.
   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.
   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.
   Stroman, R.C. 1994. Epigenesis: The missing beat in biotechnology. Biotechnology 12:156‐163.
   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.
   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.
   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.
   Tost, J. and Gut, I.G. 2002. Genotyping single nucleotide polymorphisims by mass spectrometry. Mass Spectrom. Rev. 21:388‐418.
   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.
   van den Boom, D., Jurinke, C., Higgins, S., Becker, T., and Koster, H. 1998. Mass spectrometric DNA diagnostics. Nucleosides Nucleotides 17:2157‐2164.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
   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.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library