Chapter 3 Comparative Sequence Analysis by MALDI-TOF Mass Spectrometry - Utilizing the Known to Discover the New

Perspectives in Bioanalysis

Volumn 2, Issue , 2007, Pages 97-117

  Ehrich, Mathias ^a   Hillenkamp, Franz ^b   Boom, Dirk van den ^a  

^a SEQUENOM INC   (United States)

^b UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 44349143849     PISSN: 18710069     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1871-0069(06)02003-9     Document Type: Review

References (46)

1. Abdi F., Bradbury E.M., Doggett N., and Chen X. Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags. Nucleic Acids Res. 29 13 (2001) e61
2. Abdi F.A., Mundt M., Doggett N., Bradbury E.M., and Chen X. Validation of DNA sequences using mass spectrometry coupled with nucleoside mass tagging. Genome Res. 12 7 (2002) 1135-1141
3. Bennett S.T., Barnes C., Cox A., Davies L., and Brown C. Toward the $1,000 human genome. Pharmacogenomics 6 4 (2005) 373-382
4. Berkenkamp, S., Hillenkamp, F. and van den Boom, D., (2003). Orthogonal ion extraction MALDI-TOF with a single-quadrupole. In: Features and Applications for DNA/RNA Analysis. International Conference of the American Society of Mass Spectrometry (ASMS), Montreal, Canada, Extended Abstract.
5. Bocker S. SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. Bioinformatics 19 Suppl 1 (2003) I44-I53
6. Bocker S. Sequencing from compomers: using mass spectrometry for DNA de novo sequencing of 200+ nt. J. Comput. Biol. 11 6 (2004) 1110-1134
7. Clark S.J., Harrison J., Paul C.L., and Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22 15 (1994) 2990-2997
8. Costello J.F., Fruhwald M.C., Smiraglia D.J., Rush L.J., Robertson G.P., Gao X., Wright F.A., Feramisco J.D., Peltomaki P., Lang J.C., Schuller D.E., Yu L., Bloomfield C.D., Caligiuri M.A., Yates A., Nishikawa R., Su Huang H., Petrelli N.J., Zhang X., O'Dorisio M.S., Held W.A., Cavenee W.K., and Plass C. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24 2 (2000) 132-138
9. Costello J.F., and Plass C. Methylation matters. J. Med. Genet. 38 5 (2001) 285-303
10. Ehrich M., Bocker S., and van den Boom D. Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS. Nucleic Acids Res. 33 4 (2005) e38
11. Ehrich M., Nelson M.R., Stanssens P., Zabeau M., Liloglou T., Xinarianos G., Cantor C.R., Field J.K., and van den Boom D. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102 44 (2005) 15785-15790
12. Elso C., Toohey B., Reid G.E., Poetter K., Simpson R.J., and Foote S.J. Mutation detection using mass spectrometric separation of tiny oligonucleotide fragments. Genome Res. 12 9 (2002) 1428-1433
13. Etzioni R., Urban N., Ramsey S., McIntosh M., Schwartz S., Reid B., et al. The case for early detection. Nat. Rev. Cancer 3 4 (2003) 243-252
14. Feinberg A.P. Cancer epigenetics takes center stage. Proc. Natl. Acad. Sci. USA 98 2 (2001) 392-394
15. Fenn J.B., Mann M., Meng C.K., Wong S.F., and Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 246 (1989) 246
16. Gut I.G. DNA analysis by MALDI-TOF mass spectrometry. Hum. Mutat. 23 5 (2004) 437-441
17. Hahner S., Ludemann H.C., Kirpekar F., Nordhoff E., Roepstorff P., Galla H.J., and Hillenkamp F. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) of endonuclease digests of RNA. Nucleic Acids Res. 25 10 (1997) 1957-1964
18. Hahner S., Schneider A., Ingendoh A., and Mosner J. Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry. Nucleic Acids Res. 28 (2000) 18
19. Hartmer R., Storm N., Boecker S., Rodi C.P., Hillenkamp F., Jurinke C., et al. RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucleic Acids Res. 31 9 (2003) e47
20. Herman J.G., Graff J.R., Myohanen S., Nelkin B.D., and Baylin S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93 18 (1996) 9821-9826
21. Honisch C., Raghunathan A., Cantor C.R., Palsson B.O., and van den Boom D. High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12. Genome Res. 14 12 (2004) 2495-2502
22. Jones P.A., and Baylin S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3 6 (2002) 415-428
23. Jurinke C., Oeth P., and Van Den Boom D. MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis. Mol. Biotechnol. 26 2 (2004) 147-164
24. Karas M., and Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 Daltons. Anal. Chem. 60 20 (1988) 2299-2301
25. Kartalov E.P., and Quake S.R. Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis. Nucleic Acids Res. 32 9 (2004) 2873-2879
26. Kling J. Ultrafast DNA sequencing. Nat. Biotechnol. 21 12 (2003) 1425-1427
27. Krebs S., Medugorac I., Seichter D., and Forster M. RNaseCut: a MALDI mass spectrometry-based method for SNP discovery. Nucleic Acids Res. 31 7 (2003) e37
28. Lai E., Riley J., Purvis I., and Roses A. A 4-Mb high-density single nucleotide polymorphism-based map around human APOE. Genomics 54 1 (1998) 31-38
29. Laird P.W. The power and the promise of DNA methylation markers. Nat. Rev. Cancer 3 4 (2003) 253-266
30. Lefmann M., Honisch C., Bocker S., Storm N., von Wintzingerode F., Schlotelburg C., Moter A., van den Boom D., and Gobel U.B. Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J. Clin. Microbiol. 42 1 (2004) 339-346
31. Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat. Rev. Genet. 3 9 (2002) 662-673
32. Loboda A.V., Ackloo S., and Chernushevich I.V. A high-performance matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer with collisional cooling. Rapid Commun. Mass Spectrom. 17 22 (2003) 2508-2516
33. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., Zhang Q., Zhou J., Zurth K., Caugant D.A., Feavers I.M., Achtman M., and Spratt B.G. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95 6 (1998) 3140-3145
34. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F., and Rothberg J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 7057 (2005) 376-380
35. Pomerantz S.C., Kowalak J.A., and McCloskey J.A. Determination of oligonucleotide composition from mass spectrometrically measured molecular weight. J. Am. Soc. Mass Spectrom. 4 (1993) 204-209
36. Pradhan S., Bacolla A., Wells R.D., and Roberts R.J. Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation. J. Biol. Chem. 274 46 (1999) 33002-33010
37. Shchepinov M.S., Denissenko M.F., Smylie K.J., Worl R.J., Leppin A.L., Cantor C.R., and Rodi C.P. Matrix-induced fragmentation of P3′-N5′ phosphoramidate-containing DNA: high-throughput MALDI-TOF analysis of genomic sequence polymorphisms. Nucleic Acids Res. 29 18 (2001) 3864-3872
38. Stanssens P., Zabeau M., Meersseman G., Remes G., Gansemans Y., Storm N., Hartmer R., Honisch C., Rodi C.P., Bocker S., and van den Boom D. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res. 14 1 (2004) 126-133
39. Szyf M., and Detich N. Regulation of the DNA methylation machinery and its role in cellular transformation. Prog. Nucleic Acid Res. Mol. Biol. 69 (2001) 47-79
40. Tang K., Shahgholi M., Garcia B.A., Heaney P.J., Cantor C.R., Scott L.G., and Williamson J.R. Improvement in the apparent mass resolution of oligonucleotides by using 12C/14N-enriched samples. Anal. Chem. 74 1 (2002) 226-231
41. Tost J., and Gut I.G. Genotyping single nucleotide polymorphisms by MALDI mass spectrometry in clinical applications. Clin. Biochem. 38 4 (2005) 335-350
42. Tsou J.A., Hagen J.A., Carpenter C.L., and Laird-Offringa I.A. DNA methylation analysis: a powerful new tool for lung cancer diagnosis. Oncogene 21 35 (2002) 5450-5461
43. Urwin R., and Maiden M.C. Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol. 11 10 (2003) 479-487
44. von Wintzingerode F., Bocker S., Schlotelburg C., Chiu N.H., Storm N., Jurinke C., Cantor C.R., Gobel U.B., and van den Boom D. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc. Natl. Acad. Sci. USA 99 10 (2002) 7039-7044
45. Walsh C.P., Chaillet J.R., and Bestor T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20 2 (1998) 116-117
46. Woese C.R. Bacterial evolution. Microbiol. Rev. 51 2 (1987) 221-271