Matrix layer sample preparation: An improved MALDI-MS peptide analysis method for proteomic studies

Proteomics

Volumn 8, Issue 13, 2008, Pages 2583-2595

  Garaguso, Ignazio ^a   Borlak, Jürgen ^a,b  

^a FRAUNHOFER INSTITUTE FOR TOXICOLOGY AND EXPERIMENTAL MEDICINE   (Germany)

^b HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

2,5 Dihydroxybenzoic acid; MALDI MS; Phosphorylation; Protein identification; Sample preparation

Indexed keywords

BENZOIC ACID DERIVATIVE; PEPTIDE; PHOSPHOPEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; AUTOANALYSIS; LUNG PARENCHYMA; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHODOLOGY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEOMICS; STANDARD; STATISTICAL ANALYSIS; TWO DIMENSIONAL ELECTROPHORESIS;

ANIMALS; LUNG; MICE; PEPTIDE MAPPING; PEPTIDES; PHOSPHORYLATION; PROTEOME; PROTEOMICS; REFERENCE STANDARDS; SENSITIVITY AND SPECIFICITY; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SURFACE-ACTIVE AGENTS;

EID: 47249106077     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200701147     Document Type: Article

References (37)

1. Karas, M., Hillenkamp, F., Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 1988, 60, 2299-2301.
2. Karas, M., Ingendoh, A., Bahr, U., Hillenkamp, F., Ultraviolet-laser desorption/ionization mass spectrometry of femtomolar amounts of large proteins. Biomed. Environ. Mass Spectrom. 1989, 18, 841-843.
3. Beavis, R. C., Chaudhary, T., Chait, B. T., α-cyano-4- hydroxycinnamic acid as a matrix for matrix-assisted laser desorption mass spectrometry. Org. Mass Spectrom. 1992, 27, 156-158.
4. Strupat, K., Karas, M., Hillenkamp, F., 2,5-Dihydroxybenzoic acid: A new matrix for laser desorption-ionization mass spectrometry. Int. J. Mass Spectrom. Ion Process. 1991, 111, 89.
5. Cohen, S. L., Chait, B. T., Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins. Anal. Chem. 1996, 68, 31-37.
6. Önnerfjord, P., Ekstrom, S., Bergquist, J., Nilsson, J. et al., Homogeneous sample preparation for automated high throughput analysis with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1999, 13, 315-322.
7. Andalo, C., Bocchini, P., Pozzi, R., Galletti, G. C., Accurate mass measurement of synthetic analogues of prazosine by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2001, 15, 665-669.
8. Cohen, L. H., Gusev, A. I., Small molecule analysis by MALDI mass spectrometry. Anal. Bioanal. Chem. 2002, 373, 571-586.
9. Nicola, A. J., Gusev, A. I., Proctor, A., Jackson, E. K., Hercules D. M., Application of the fast-evaporation sample preparation method for improving quantification of angiotensin II by matrix-assisted laser desorption/ionization. Rapid Commun. Mass Spectrom. 1995, 9, 1164-1171.
10. Stoeckli, M., Farmer, T. B., Caprioli, R. M., Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument. J. Am. Soc. Mass Spectrom. 1999, 10, 67-71.
11. Anderson, N. L., Anderson, N. G., The human plasma proteome: History, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1, 845-867.
12. Lisacek, F. C., Traini, M. D., Sexton, D., Harry, J. L., Wilkins, M. R., Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting. Proteomics 2001, 1, 186-193.
13. Claverol, S., Burlet-Schiltz, O., Girbal-Neuhauser, E., Gairin, J. E., Monsarrat, B., Mapping and structural dissection of human 20 S proteasome using proteomic approaches. Mol. Cell. Proteomics 2002, 1, 567-578.
14. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F. et al., Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. USA 1996, 93, 14440-14445.
15. Juhasz, P., Costello, C. E., Biemann, K., Matrix-assisted laser desorption ionization mass spectrometry with 2-(hydroxyphenyl-azolbenzoic acid matrix. J Am. Soc. Mass Spectrom. 1993, 4, 399-409.
16. Vorm, O., Roepstorff, P., Mann, M., Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation. Anal. Chem. 1994, 66, 3281-3287.
17. Kussmann, M., Nordhoff, E., Rahbek-Nielsen, H., Haebel, S. et al., Matrix-assisted laser desorption/ionization mass spectrometry sample preparation techniques designed for various peptide and protein analytes. J. Mass Spectrom. 1997, 32, 593-601.
18. Dai, Y. Q., Whittal, R. M., Li, L., Confocal fluorescence microscopic imaging for investigating the analyte distribution in MALDI matrices. Anal. Chem. 1996, 68, 2494-2500.
19. Kjellstrom, S., Jensen, O. N., Phosphoric acid as a matrix additive for MALDI MS analysis of phosphopeptides and phosphoproteins. Anal. Chem. 2004, 76, 5109-5117.
20. Garden, R. W., Sweedler, J. V., Heterogeneity within MALDI samples as revealed by mass spectrometric imaging. Anal. Chem. 2000, 72, 30-36.
21. Schuerenberg, M., Luebbert, C., Eickhoff, H., Kalkum, M. et al., Prestructured MALDI-MS sample supports. Anal. Chem. 2000, 72, 3436-3442.
22. Johnson, T., Berquist, J., Ekman, R., Nordhoff, E. et al., A CEMALDI interface based on the use of prestructured sample supports. Anal. Chem. 2001, 73, 1670-1675.
23. Stone, K. L., LoPresti, M. B., Crawford, J. M., DeAngelis, R., Williams, K. R. A, in: Matsudaira, P. (Ed.), Practical Guide to Protein and Peptide Purification for Microsequencing, Academic Press, NY 1989, pp. 33-47.
24. Doherty, N. S., Littman, B. H., Reilly, K., Swindell, A. C. et al., Analysis of changes in acute-phase plasma proteins in an acute inflammatory response and in rheumatoid arthritis using two-dimensional gel electrophoresis. Electrophoresis 1998, 19, 355-363.
25. Ferrari, G., Garaguso, I., Adu-Bobie, J., Doro, F. et al., Outer membrane vesicles from group B Neisseria meningitidis delta gna33 mutant: Proteomic and immunological comparison with detergent-derived outer membrane vesicles. Proteomics 2006, 6, 1856-1866.
26. Jensen, O. N., Wilm, M., Shevchenko, A., Mann, A., Peptide sequencing of 2-DE gel-isolated proteins by nanoelectrospray tandem mass spectrometry. Methods Mol. Biol. 1999, 112, 571-588.
27. Wilm, M., Shevchenko, A., Houthaeve, T., Breit, S. et al., Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 1996, 379, 466-469.
28. Nordhoff, E., Schürenberg, M., Thiele, G., Lübberta, C. et al., Sample preparation protocols for MALDI-MS of peptides and oligonucleotides using prestructured sample supports Int. J. Mass Spectrom. 2003, 226, 163-180.
29. Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
30. Gobom, J., Nordhoff, E., Mirgorodskaya, E., Ekman, R., Roepstorff, P., Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J. Mass Spectrom. 1999, 34, 105-116.
31. Gusev, A. I., Wilkinson, W. R., Proctor, A., Hercules, D. M., Improvement of signal reproducibility and matrix/comatrix effects in MALDI analysis. Anal. Chem. 1995, 67, 1034-1041.
32. Horneffer, V., Dreisewerd, K., Ludemann, H. C., Hillenkamp, F. et al., Is the incorporation of analytes into matrix crystals a prerequisite for matrix-assisted laser desorptionionization mass spectrometry? A study of five positional isomers of dihydroxybenzoic acid. Int. J. Mass Spectrom. 1999, 187, 859-870.
33. Kruger, R., Pfenninger, A., Fournier, I., Gluckmann, M., Karas, M., Analyte incorporation and ionization in matrix-assisted laser desorption/ionization visualized by pH indicator molecular probes. Anal. Chem. 2001, 73, 5812-5821.
34. Cordero, M. M., Cornish, T. J., Lys, I. A., Cotter, R. J., Sequencing peptides without scanning the reflectron: Post-source decay with a curved-field reflectron time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 1995, 9, 1356-1361.
35. Karas, M., Bahr, U., Strupat, K., Hillenkamp, F. et al., Matrix dependence of metastable fragmentation of glycoproteins in MALDI TOF mass spectrometry. Anal. Chem. 1995, 67, 675-679.
36. Bagshaw, R. D., Callahan, J. W., Mahuran, D. J., Desalting of in-gel-digested protein sample with mini-C18 columns for matrix-assisted laser desorption ionization time of flight peptide mass fingerprinting. Anal. Biochem. 2000, 284, 432-435.
37. Stensballe, A., Andersen, S., Jensen, O. N., Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off-line mass spectrometry analysis. Proteomics 2001, 1, 207-222.