The essence of DNA sample preparation for MALDI mass spectrometry

Journal of Biochemical and Biophysical Methods

Volumn 70, Issue 2, 2007, Pages 311-318

  Sauer, Sascha ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

DNA; MALDI; Matrix; Oligonucleotide; Purification; SNP

Indexed keywords

2 THIO 6 AZATHYMINE; 2,3,4 TRIHYDROXYACETOPHENONE; 2,4,6 TRIHYDROXYACETOPHENONE; 3 HYDROXYPICOLINIC ACID; ACETOPHENONE DERIVATIVE; ALPHA CYANO 4 HYDROXYCINNAMIC ACID; ALPHA CYANO 4 HYDROXYCINNAMIC ACID METHYL ESTER; ANTHRANILIC ACID; CINNAMIC ACID DERIVATIVE; DNA; DNA FRAGMENT; FERULIC ACID; GENTISIC ACID; PICOLINIC ACID DERIVATIVE; SALICYLAMIDE; THYMINE DERIVATIVE; UNCLASSIFIED DRUG;

ANALYTIC METHOD; CHEMICAL MODIFICATION; DNA DETERMINATION; DNA MODIFICATION; DNA PURIFICATION; DNA SEQUENCE; GENOMICS; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; TIME OF FLIGHT MASS SPECTROMETRY; ULTRAVIOLET RADIATION; YAG LASER;

CHROMATOGRAPHY; DNA; DNA FINGERPRINTING; SOLID PHASE MICROEXTRACTION; SPECIMEN HANDLING; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33847249336     PISSN: 0165022X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbbm.2006.10.007     Document Type: Review

References (47)

1. Karas M., and Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10000 daltons. Anal Chem 60 (1988) 2299-2303
2. Sauer S. Typing of single nucleotide polymorphisms by MALDI mass spectrometry: principles and diagnostic applications. Clin Chim Acta 363 (2006) 95-105
3. Karas M., Gluckmann M., and Schafer J. Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors. J Mass Spectrom 35 (2000) 1-12
4. Gut I.G. DNA analysis by MALDI-TOF mass spectrometry. Hum Mutat 23 (2004) 437-441
5. Corona G., and Toffoli G. High throughput screening of genetic polymorphisms by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Comb Chem High Throughput Screen 7 (2004) 707-725
6. Jurinke C., Denissenko M.F., Oeth P., Ehrich M., van den Boom D., and Cantor C.R. A single nucleotide polymorphism based approach for the identification and characterization of gene expression modulation using MassARRAY. Mutat Res 573 (2005) 83-95
7. Sauer S., and Gut I.G. Genotyping single-nucleotide polymorphisms by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 782 (2002) 73-87
8. Christian N.P., Reilly J.P., Mokler V.R., Wincott F.E., and Ellington A.D. Elucidation of the initial step of oligonucleotide fragmentation in matrix-assisted laser desorption/ionization using modified nucleic acids. J Am Soc Mass Spectrom 12 (2001) 744-753
9. Nordhoff E., Kirpekar F., Karas M., Cramer R., Hahner S., Hillenkamp F., et al. Comparison of IR- and UV-matrix-assisted laser desorption/ionization mass spectrometry of oligodeoxynucleotides. Nucleic Acids Res 22 (1994) 2460-2465
10. Griffin T.J., and Smith L.M. Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry. Trends Biotechnol 18 (2000) 77-84
11. Juhasz P., Roskey M.T., Smirnov I.P., Haff L.A., Vestal M.L., and Martin S.A. Applications of delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry to oligonucleotide analysis. Anal Chem 68 (1996) 941-946
12. Ross P., Hall L., and Haff L.A. Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 29 (2000) 620-629
13. Pieles U., Zuercher W., Schaer M., and Moser H.E. Matrix-assisted laser desorption time-of-flight mass spectrometry: a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucleic Acids Res 14 (1993) 3191-3196
14. Fu D.J., Tang K., Braun A., Reuter D., Darnhofer-Demar B., Little D.P., et al. Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat Biotechnol 16 (1998) 381-384
15. Hilton G.C., Martinis D.A., Wollman K.D., Irwin L.L., Dulcie D., Gerber P.M., et al. Impact energy measurement in time-of-flight mass spectrometry with cryogenic micro-calorimeters. Nature 391 (1998) 672-675
16. Zhu Y.F., Chung C.N., Taranenko N.I., Allman S.L., Martin S.A., Haff L., et al. The study of 2,3,4-trihydroxyacetophenone and 2,4,6-trihydroxyacetophenone as matrices for DNA detection in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom 10 (1996) 383-388
17. Wu K.J., Steding A., and Becker C.H. 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 (1993) 142-146
18. Lecchi P., Le H.M.T., and Pannell L.K. 6-Aza-2-thiothymine: a matrix for MALDI spectra of oligonucleotides. Nucleic Acids Res 23 (1995) 1276-1277
19. Shahgholi M., Garcia B.A., Chiu N.H., Heaney P.J., and Tang K. Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved. Nucleic Acids Res 29 (2001) e91
20. Beavis R.C., and Chait B.T. Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins. Rapid Commun Mass Spectrom 3 (1989) 432-435
21. Koomen J.M., and Russell D.H. Ultraviolet/matrix-assisted laser desorption/ionization mass spectrometric characterization of 2,5-dihydroxybenzoic acid-induced reductive hydrogenation of oligonucleotides on cytosine residues. J Mass Spectrom 35 (2000) 1025-1034
22. Tang W., Zhu L., and Smith L.M. Controlling DNA Fragmentation in MALDI-MS by chemical modification. Anal Chem 69 (1997) 302-312
23. Schneider K., and Chait B.T. Increased stability of nucleic acids containing 7-deaza-guanosine and 7-deaza-adenosine may enable rapid DNA sequencing by matrix-assisted laser desorption mass spectrometry. Nucleic Acids Res 23 (1995) 1570-1575
24. Kirpekar F., Nordhoff E., Kristiansen K., Roepstorff P., Hahner S., and Hillenkamp F. 7-Deaza purine bases offer a higher ion stability in the analysis of DNA by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 9 (1995) 525-531
25. Nordhoff E., Cramer R., Karas M., Hillenkamp F., Kirpekar F., Kristiansen K., et al. Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Res 21 (1993) 3347-3357
26. Ono T., Scalf M., and Smith L.M. 2'-Fluoro modified nucleic acids: polymerase-directed synthesis, properties and stability to analysis by matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Res 25 (1997) 4581-4588
27. Gut I.G., Jeffery W.A., Pappin D.J.C., and Beck S. Analysis of DNA by 'charge tagging' and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 11 (1997) 43-50
28. Sauer S., and Gut I.G. Extension of the GOOD assay for genotyping single nucleotide polymorphisms by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 17 (2003) 1265-1272
29. Gobom J., Schuerenberg M., Mueller M., Theiss D., Lehrach H., and Nordhoff E. Alpha-cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal Chem 73 (2001) 434-438
30. Sauer S., Lechner D., Berlin K., Lehrach H., Escary J.L., Fox N., et al. A novel procedure for efficient genotyping of single nucleotide polymorphisms. Nucleic Acids Res 28 (2000) e13
31. Li J., Butler J.M., Tan Y., Lin H., Royer S., Ohler L., et al. Single nucleotide polymorphism determination using primer extension and time-of-flight mass spectrometry. Electrophoresis 20 (1999) 1258-1265
32. Wenzel T., Elssner T., Fahr K., Bimmler J., Richter S., Thomas I., et al. Genosnip: SNP genotyping by MALDI-TOF MS using photocleavable oligonucleotides. Nucleosides Nucleotides Nucleic Acids 22 (2003) 1579-1581
33. Sauer S., Lehrach H., and Reinhardt R. MALDI mass spectrometry analysis of single nucleotide polymorphisms by photocleavage and charge-tagging. Nucleic Acids Res 31 (2003) e63
34. Bauer O., Guerasimova A., Sauer S., Thamm S., Steinfath M., Herwig R., et al. Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 18 (2004) 1821-1829
35. Sauer S., Gelfand D.H., Boussicault F., Bauer K., Reichert F., and Gut I.G. Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry. Nucleic Acids Res 30 (2002) e22
36. Little D.P., Cornish T.J., O'Donnell M.J., Braun A., Cotter R.J., Koster H., et al. MALDI on a chip: analysis of low-to subfemtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipette. Anal Chem 69 (1997) 4540-4546
37. Schuerenberg M., Luebbert C., Eickhoff H., Kalkum M., Lehrach H., and Nordhoff E. Prestructured MALDI-MS sample supports. Anal Chem 72 (2000) 3436-3442
38. Buetow K.H., Edmonson M., MacDonald R., Clifford R., Yip P., Kelley J., et al. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci U S A 98 (2001) 581-584
39. Sauer S., Kepper P., Smyra A., Dahl A., Ferse F.T., Lehrach H., et al. Automated solid-phase extraction for purification of single nucleotide polymorphism genotyping products prior to matrix-assisted laser desorption/ionisation time-of-flight mass spectrometric analysis. J Chromatogr A 1049 (2004) 9-16
40. Mengel-Jorgensen J., Sanchez J.J., Borsting C., Kirpekar F., and Morling N. MALDI-TOF mass spectrometric detection of multiplex single base extended primers. A study of 17 y-chromosome single-nucleotide polymorphisms. Anal Chem 76 (2004) 6039-6045
41. Storm N., Darnhofer-Patel B., van den Boom D., and Rodi C.P. MALDI-TOF mass spectrometry-based SNP genotyping. Methods Mol Biol 212 (2003) 241-262
42. Xu Y., Bruening M.L., and Watson J.T. Non-specific, on-probe cleanup methods for MALDI-MS samples. Mass Spectrom Rev 22 (2003) 429-440
43. Kepper P., Reinhardt R., Dahl A., Lehrach H., and Sauer S. Matrix-assisted laser desorption/ionisation mass spectrometry analysis of DNA on micro-arrays. Clin Chem 52 (2006) 1303-1310
44. Sauer S., Lange B.M., Gobom J., Nyarsik L., Seitz H., and Lehrach H. Miniaturization in functional genomics and proteomics. Nat Rev Genet 6 (2005) 465-476
45. Bernad Jr. P.L., Khan S., Korshun V.A., Southern E.M., and Shchepinov M.S. S(O)-pixyl protecting group as efficient mass-tag. Chem Commun 27 (2005) 3466-3468
46. Wei J., Buriak J.M., and Siuzdak G. Desorption-ionization mass spectrometry on porous silicon. Nature 399 (1999) 243-246
47. Fu Y., Xu S., Pan C., Ye M., Zou H., and Guo B. A matrix of 3,4-diaminobenzophenone for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Nucleic Acids Res 34 (2006) e94