Mass Spectrometry: Sample Preparation for the Application of MALDI Mass Spectrometry in Proteome Analysis

Proteomics Sample Preparation

Volumn , Issue , 2008, Pages 73-94

  Tholey, Andreas ^a   Glückmann, Matthias ^b   Seemann, Kerstin ^c   Karas, Michael ^d  

^a SAARLAND UNIVERSITY   (Germany)

^b Applied Biosystems   (Germany)

^c MERCK KGAA   (Germany)

^d GOETHE UNIVERSITY   (Germany)

Author keywords

Application; Body fluids; Differential proteome analysis; Electrospray ionization; Fourier transform ion cyclotron mass spectrometry; Label free proteomic analyses; Labelling technologies; MALDI mass spectrometry; Mass spectrometry; Membrane protein localization; Methods; Proteome analysis; Proteomics sample preparation; Stable isotope tagging; Subcellular compartments

Indexed keywords

EID: 84889792032     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527622832.ch4     Document Type: Chapter

References (53)

1. Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem., 60, 2299-2301.
2. Cohen, L.H. and Gusev, A.I. (2002) Small molecule analysis by MALDI mass spectrometry. Anal. Bioanal. Chem., 373, 571-586.
3. Dreisewerd, K. (2003) The desorption process in MALDI. Chem. Rev., 103, 395-426.
4. Karas, M. and Kruger, R. (2003) Ion formation in MALDI: the cluster ionization mechanism. Chem. Rev., 103, 427-440.
5. Knochenmuss, R. and Zenobi, R. (2003) MALDI ionization: the role of in-plume processes. Chem. Rev., 103, 441-452.
6. Colby, S.M., King, T.B., Reilly, J.P. and Lubman, D.M. (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.
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 linear time-of-flight mass spectrometer. Anal. Chem., 67, 1998-2003.
8. Horneffer, V., Gluckmann, M., Kruger, R., Karas, M., Strupat, K. and Hillenkamp, F. (2006) Matrix-analyteinteraction in MALDI MS: pellet and nano-electrospray preparations. Int. J. Mass Spectrom., 249/250, 426-432.
9. Schleuder, D., Hillenkamp, F. and Strupat, K. (1999) IR-MALDI-mass analysis of electroblotted proteins directly from the membrane: comparison of different membranes application to on-membrane digestion, and protein identification by database searching. Anal. Chem., 71, 3238-3247.
10. Ehring, H., Karas, M. andHillenkamp, F. (1992) Role of photoionization and photochemistry in ionization processes of organic molecules and relevance for matrix-assisted laser desorption ionization mass spectrometry. Org. Mass Spectrom., 27, 472-480.
11. Beavis, R.C. and Chait, B.T. (1989) Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins. Rapid Commun. Mass Spectrom., 3, 432-435.
12. Beavis, R.C., Chaudhary, T. and Chait, B. T. (1992) Alpha-cyano-4-hydroxycinnamic acid as a matrix for matrix assisted laser desorption mass spectrometry. Org. Mass Spectrom., 27, 156-158.
13. Strupat, K., Karas, M. and Hillenkamp, F. (1991) 25-Dihydroxy benzoic acid-a new matrix for laser desorption/ionization mass-spectrometry. Int. J. Mass Spectrom. Ion Proc., 111, 89-102.
14. Juhasz, P., Costello, C.E. and Biemann, K. (1993) Matrix assisted laser desorption ionization mass spectrometry with 2-(4- hydroxyphenylazo)benzoic acid matrix. J. Am. Soc. Mass Spectrom., 4, 399-409.
15. Pieles, U., Zurcher, W., Schar, 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.
16. Gorman, J.J., Ferguson, B.L. and Nguyen, T.B. (1996) Use of 2, 6-dihydroxyacetophenone for analysis of fragile peptides, disulphide bonding and small proteins by matrix-assisted laser desorption/ionization. Rapid Commun. Mass Spectrom., 10, 529-536.
17. Pitt, J.J. and Gorman, J.J. (1996) Matrixassisted laser desorption/ionization timeof- flight mass spectrometry of sialylated glycopeptides and proteins using 2,6- dihydroxyacetophenone as a matrix. Rapid Commun. Mass Spectrom., 10, 1786-1788.
18. 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.
19. Wu, K., Shaler, T.A. and Becker, B.T. (1994) Time-of-flight mass spectrometry of underivatized single-stranded DNA oligomers by matrix-assisted laser desorption. Anal. Chem., 66, 1637-1645.
20. Tang, K., Taranenko, N.I., Allman, S.L., Chen, C.H., Chang, L.Y. and Jacobson, K. B. (1994) Picolinic acid as a matrix for laser mass spectrometry of nucleic acids and proteins. Rapid Commun. Mass Spectrom., 8, 673-677.
21. Karas, M., Bahr, U., Strupat, K., Hillenkamp, F., Tsarbopoulos, A. and Pramanik, B.N. (1995) Matrix dependence of metastable fragmentation of glycoproteins in MALDI TOF massspectrometry. Anal. Chem., 67, 675-679.
22. Karas, M., Ehring, H., Nordhoff, E., Stahl, B., Strupat, K., Hillenkamp, F., Grehl, M. and Krebs, B. (1993) Matrix-assisted laser-desorption ionization massspectrometry with additives to 2, 5-dihydroxybenzoic acid. Org. Mass Spectrom., 28, 1476-1481.
23. Bahr, U., Stahl, B., Zeng, J., Gleitsmann, E. and Karas, M. (1997) Delayed extraction time-of-flight MALDI mass spectrometry of proteins above 25,000 Da. J. Mass Spectrom., 32, 1111-1116.
24. Laugesen, S. and Roepstorff, P. (2003) Combination of two matrices results in improved performance of MALDI MS for peptide mass mapping and protein analysis. J. Am. Soc. Mass Spectrom., 14, 992-1002.
25. Distler, A.M. and Allison, J. (2001) Improved MALDI-MS analysis of oligonucleotides through the use of fucose as a matrix additive. Anal. Chem., 73, 5000-5003.
26. Distler, A.M. and Allison, J. (2001) 5-Methoxysalicylic acid and spermine: a new matrix for the matrix-assisted laser desorption/ionization mass spectrometry analysis of oligonucleotides. J. Am. Soc. Mass Spectrom., 12, 456-562.
27. Zhang, L.K. andGross,M.L. (2000)Matrixassisted laser desorption/ionization mass spectrometry methods for oligodeoxynucleotides: improvements inmatrix detection limits, quantification, and sequencing. J.Am. Soc.Mass Spectrom., 11, 854-865.
28. Kussmann, M., Nordhoff, E., Rahbek Nielsen, H., Haebel, S., Rossel Larsen, M., Jakobsen, L., Gobom, J., Mirgorodskaya, E., Kroll Kristensen, A., Palm, L. and Roepstorff P. (1997) Matrixassisted laser desorption/ionization mass spectrometry sample preparation techniques designed for various peptide and protein analytes. J. Mass Spectrom., 32, 593-601.
29. Smirnov, I.P., Zhu, X., Taylor, T., Huang, Y., Ross, P., Papayanopoulos, I.A.,Martin, S.A. and Pappin, D.J. (2004) Suppression of alpha-cyano-4-hydroxycinnamic acid matrix clusters and reduction of chemical noise in MALDI-TOF mass spectrometry. Anal. Chem., 76, 2958-2965.
30. Kjellstrom, S. and Jensen, O.N. (2004) Phosphoric acid as a matrix additive for MALDI MS analysis of phosphopeptides and phosphoproteins. Anal. Chem., 76, 5109-5117.
31. Cohen, S.L. and Chait, B.T. (1996) Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. Anal. Chem., 68, 31-37.
32. 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.
33. Dai, Y., Whittal, R.M. and Li, L. (1999) Two-layer sample preparation: a method for MALDI-MS analysis of complex peptide and protein mixtures. Anal. Chem., 71, 1087-1091.
34. Xiang, F. and Beavis, R.C. (1994) A method to increase contaminant tolerance in protein MALDI by the fabrication of thin protein-doped polycrystalline films. Rapid Commun. Mass Spectrom., 8, 199-204.
35. Chan, T.W.D., Colburn, A.W., Derrick, P. J., Gardiner, D.J. and Bowden, M. (1992) Suppression of matrix ions in ultravioletlaser desorption-scanning electronmicroscopy and Raman-spectroscopy of the solid samples. Org. Mass Spectrom., 27, 188-194.
36. Gorisch, H. (1988) Drop dialysis: time course of salt and protein exchange. Anal. Biochem., 173, 393-398.
37. Kussmann, M., Nordhoff, E., Rahbek Nielsen, H.,Haebel, S., Rossel Larsen, M., Jakobsen, L., Gobom, J., Mirgorodskaya, E., Kroll Kristensen, A., Palm, L. and Roepstorff, P. (1997) Matrix-assisted laser desorption/ionization mass spectrometry sample preparation techniques designed for various peptide and protein analytes. J. Mass Spectrom., 32, 593-601.
38. Beranova-Giorgianni, S. and Desiderio, D.M. (2000) Mass spectrometry of the human pituitary proteome: identification of selected proteins. Rapid Commun. Mass Spectrom., 14, 161-167.
39. Rappsilber, J., Ishihama, Y. andMann, M. (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem., 75, 663-670.
40. Majors, R.E. and Shukla, A. (2005) Micropipette tip-based sample preparation for bioanalysis. LCGC North America, 23.
41. Fella, K., Gluckmann, M., Hellmann, J., Karas, M., Kramer, P.J. and Kroger, M. (2005) Use of two-dimensional gel electrophoresis in predictive toxicology: identification of potential early protein biomarkers in chemically induced hepatocarcinogenesis. Proteomics, 5, 1914-1927.
42. Ross, P.L., Huang, Y.N., Marchese, J.N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M.,He, F., Jacobson, A. and Pappin, D.J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics, 3, 1154-1169.
43. Kuhn-Holsken, E., Lenz, C., Sander, B., Luhrmann, R. and Urlaub, H. (2005) Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UVirradiated ribonucleoprotein particles. Rna, 11, 1915-1930.
44. Sinz, A., Kalkhof, S. and Ihling, C. (2005) Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometry. J. Am. Soc. Mass Spectrom., 16, 1921-1931.
45. Yanes, O., Villanueva, J., Querol, E. and Aviles, F.X. (2005) Functional screening of serine protease inhibitors in the medical leech Hirudo medicinalis monitored by intensity fading MALDITOF MS. Mol. Cell. Proteomics, 4, 1602-1613.
46. Shi, J., Koeppe, J.R., Komives, E.A. and Taylor, P. (2006) Ligand-induced conformational changes in the acetylcholine- binding protein analyzed by hydrogen-deuterium exchange mass spectrometry. J. Biol. Chem., 281, 12170-12177.
47. Juhasz, P., Papayannopulos, I.A., Zeng, C., Papov, V. and Biemann, K. (1992) The Utility of Matrix-assisted Laser Desorption for the direct Analysis of enzymatic Digests of Proteins. Proceedings of the 40th ASMS Conference on Mass Spectrometry and Allied Topics Washington, DC, USA, 1913-1914.
48. Beavis, R.C. and Chait, B.T. (1989) Matrix-assisted laser-desorption mass spectrometry using 355nm radiation. Rapid Commun. Mass Spectrom., 3, 436-439.
49. Karas, M., Nordhoff, E., Stahl, B., Strupat, K. and Hillenkamp, F. (1992) Matrix-Mixtures for a Superior Performance of Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Proceedings of the 40th ASMS Conference on Mass Spectrometry and Allied Topics Washington, DC, USA, pp. 368-369.
50. Karas, M., Bahr, U. and Stahl-Zeng, J. (1996) Large ions: their vaporization, detection and structural analysis. In: Steps Towards a More Refined Picture of the Matrix Function in UV MALDI (eds T. Baer C.Y. Ng and I. Powis), John Wiley, pp. 27.
51. Papac, D.I., Wong, A. and Jones, A.J. (1996) Analysis of acidic oligosaccharides and glycopeptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem., 68, 3215-3223.
52. Zhu, Y.F., Chung, C.N., Taranenko, N.I., Allman, S.L., Martin, S.A., Haff, L. and Chen, C.H. (1996) The study of 2,3, 4-trihydroxyacetophenone and 2,4,6- trihydroxyacetophenone as matrices for DNAdetection in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom., 10, 383-388.
53. Swiderek, K., Alpert, A., Heckendorf, A., Nugent, K. and Patterson, S. (1997) Structural analysis of proteins and peptides in the presence of detergents: Tricks of the trade. ABRF: News Methods and Reviews, December, 17-25.