An integrated approach to identifying chemically induced posttranslational modifications using comparative MALDI-MS and targeted HPLC-ESI-MS/MS

Chemical Research in Toxicology

Volumn 16, Issue 5, 2003, Pages 598-608

  Person, Maria D ^a   Monks, Terrence J ^a   Lau, Serrine S ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; BENZOQUINONE; BUTYRIC ACID; CYTOCHROME C; HISTIDINE; HISTONE H4; LYSINE; PEPTIDE FRAGMENT;

ACETYLATION; AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CELL STRAIN; CHEMICAL ANALYSIS; CONTROLLED STUDY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IN VITRO STUDY; IN VIVO STUDY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHYLATION; NONHUMAN; PROTEIN ANALYSIS; PROTEIN MODIFICATION; PROTEIN STRUCTURE; RNA TRANSLATION; TANDEM MASS SPECTROMETRY;

ANIMALIA;

EID: 0037986377     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx020109f     Document Type: Article

References (40)

1. Meri, S., and Baumann, M. (2001) Proteomics: posttranslational modifications, immune responses and current analytical tools. Biomol. Eng. 18, 213-220.
2. Zhou, H., Watts, J. D., and Aebersold, R. (2001) A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19, 375-378.
3. Annan, R. S., Huddleston, M. J., Verma, R., Deshaies, R. J., and Carr, S. A. (2001) A multidimensional electrospray MS-based approach to phosphopeptide mapping. Anal. Chem. 73, 393-404.
4. Mann, M., Ong, S. E., Gronborg, M., Steen, H., Jensen, O. N., and Pandey, A. (2002) Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 20, 261-268.
5. Raska, C. S., Parker, C. E., Dominski, Z., Marzluff, W. F., Glish, G. L., Pope, R. M., and Borchers, C. H. (2002) Direct MALDI-MS/MS of phosphopeptides affinity-bound to immobilized metal ion affinity chromatography beads. Anal. Chem. 74, 3429-3433.
6. Kim, J. Y., Kim, K. W., Kwon, H. J., Lee, D. W., and Yoo, J. S. (2002) Probing lysine acetylation with a modification-specific marker ion using high-performance liquid chromatography/electrospray-mass spectrometry with collision-induced dissociation. Anal. Chem. 74, 5443-5449.
7. Apffel, A., Chakel, J. A., Hancock, W. S., Souders, C., M'Timkulu, T., and Pungor, E., Jr. (1996) Application of high-performance liquid chromatograph-electrospray ionization mass spectrometry and matrix-assisted laser-desorption ionization time-of-flight mass spectrometry in combination with selective enzymatic modifications in the characterization of glycosylation patterns in single-chain plasminogen activator. J. Chromatogr. A 732, 27-42.
8. Banks, G. C., Li, Y., and Reeves, R. (2000) Differential in vivo modifications of the HMGI(Y) nonhistone chromatin proteins modulate nucleosome and DNA interactions. Biochemistry 39, 8333-8346.
9. Cook, L. A., Schey, K. L., Wilcox, M. D., Dingus, J., and Hildebrandt, J. D. (1998) Heterogeneous processing of a G protein gamma subunit at a site critical for protein and membrane interactions. Biochemistry 37, 12280-12286.
10. Person, M. D., Brown, K. C., Mahrus, S., Craik, C. S., and Burlingame, A. L. (2001) Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer. Protein Sci. 10, 1549-1562.
11. Powell, K. A., Valova, V. A., Malladi, C. S., Jensen, O. N., Larsen, M. R., and Robinson, P. J. (2000) Phosphorylation of dynamin I on Ser-795 by protein kinase C blocks its association with phospholipids. J. Biol. Chem. 275, 11610-11617.
12. Kilz, S., Budzikiewicz, H., and Waffenschmidt, S. (2002) In-gel deglycosylation of sodiumdodecyl sulfate polyacrylamide gel electrophoresis-separated glycoproteins for carbohydrate estimation by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Mass Spectrom. 37, 331-335.
13. Iwafune, Y., Kawasaki, H., and Hirano, H. (2002) Electrophoretic analysis of phosphorylation of the yeast 20S proteasome. Electrophoresis 23, 329-338.
14. Lim, A., Prokaeva, T., McComb, M. E., O'Connor, P. B., Theberge, R., Connors, L. H., Skinner, M., and Costello, C. E. (2002) Characterization of transthyretin variants in familial transthyretin amyloidosis by mass spectrometric peptide mapping and DNA sequence analysis. Anal. Chem. 74, 741-751.
15. Zhang, X., Herring, C. J., Romano, P. R., Szczepanowska, J., Brzeska, H., Hinnebusch, A, G., and Qin, J. (1998) Identification of phosphorylation sites in proteins separated by polyacrylamide gel electrophoresis. Anal. Chem. 70, 2050-2059.
16. Zhang, K., Tang, H., Huang, L., Blankenship, J. W., Jones, P. R., Xiang, F., Yau, P. M., and Burlingame, A. L. (2002) Identification of Acetylation and Methylation Sites of Histone H3 from Chicken Erythrocytes by High-Accuracy Matrix-Assisted Laser Desorption Ionization-Time-of-Flight, Matrix-Assisted Laser Desorption Ionization-Postsource Decay, and Nanoelectrospray Ionization Tandem Mass Spectrometry. Anal. Biochem. 306, 259-269.
17. Zhang, K., Williams, K. E., Huang, L., Yau, P., Siino, J. S., Bradbury, E. M., Jones, P. R., Minch, M. J., and Burlingame, A. L. (2002) Histone Acetylation and Deacetylation: Identification of Acetylation and Methylation Sites of HeLa Histone H4 by Mass Spectrometry. Mol. Cell Proteomics 1, 500-508.
18. Medzihradszky, K. F., Campbell, J. M., Baldwin, M. A., Falick, A. M., Juhasz, P., Vestal, M. L., and Burlingame, A. L. (2000) The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal. Chem. 72, 552-558.
19. Loboda, A. V., Krutchinsky, A. N., Bromirski, M., Ens, W., and Standing, K. G. (2000) A tandem quadrupole/time-of-flight mass spectrometer with a matrix-assisted laser desorption/ionization source: design and performance. Rapid Commun. Mass Spectrom. 14, 1047-1057.
20. Shevchenko, A., Loboda, A., Ens, W., and Standing, K. G. (2000) MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Anal. Chem. 72, 2132-2141.
21. Lee, C. H., McComb, M. E., Bromirski, M., Jilkine, A., Ens, W., Standing, K. G., and Perreault, H. (2001) On-membrane digestion of beta-casein for determination of phosphorylation sites by matrix-assisted laser desorption/ionization quadrupole/time-off light mass spectrometry. Rapid Commun. Mass Spectrom. 15, 191-202.
22. Wilkins, M. R., Gasteiger, E., Gooley, A. A., Herbert, B. R., Molloy, M. P., Binz, P. A., Ou, K., Sanchez, J. C., Bairoch, A., Williams, K. L., and Hochstrasser, D. F. (1999) High-throughput mass spectrometric discovery of protein posttranslational modifications. J. Mol. Biol. 289, 645-657.
23. MacCoss, M. J., McDonald, W. H., Saraf, A., Sadygov, R., Clark, J. M., Tasto, J. J., Gould, K. L., Wolters, D., Washburn, M., Weiss, A., Clark, J. I., and Yates, J. R., III. (2002) Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. U.S.A. 99, 7900-7905.
24. Hansen, B. T., Jones, J. A., Mason, D. E., and Liebler, D. C. (2001) SALSA: a pattern recognition algorithm to detect electrophile-adducted peptides by automated evaluation of CID spectra in LCMS-MS analyses. Anal. Chem. 73, 1676-1683.
25. Liebler, D. C., Hansen, B. T., Davey, S. W., Tiscareno, L., and Mason, D. E. (2002) Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. Anal. Chem. 74, 203-210.
26. Liebler, D. C. (2002) Proteomic approaches to characterize protein modifications: new tools to study the effects of environmental exposures. Environ. Health Perspect. 110 (Suppl. 1), 3-9.
27. Gatlin, C. L., Eng, J. K., Cross, S. T., Detter, J. C., and Yates, J. R., III. (2000) Automated identification of amino acid sequence variations in proteins by HPLC/microspray tandem mass spectrometry. Anal. Chem. 72, 757-763.
28. Jenuwein, T., and Allis, C. D. (2001) Translating the histone code. Science 293, 1074-1080.
29. Van Holde, K. E. (1989) Histone Modifications. Chromatin, pp 111-148, Springer-Verlag, New York.
30. Monks, T. J., Hanzlik, R. P., Cohen, G. M., Ross, D., and Graham, D. G. (1992) Quinone chemistry and toxicity. Toxicol. Appl. Pharmacol. 112, 2-16.
31. Li, P., Nijhawan, D., Budihardjo, I., Srinivasula, S. M., Ahmad, M., Alnemri, E. S., and Wang, X. (1997) Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell 91, 479-489.
32. Liu, X., Kim, C. N., Yang, J., Jemmerson, R., and Wang, X. (1996) Induction of apoptotic program in cell-free extracts: requirement for dATP and cytochrome c. Cell 86, 147-157.
33. Rosenfeld, J., Capdevielle, J., Guillemot, J. C., and Ferrara, P. (1992) In-gel digestion of proteins for internal sequence analysis after one- or two-dimensional gel electrophoresis. Anal. Biochem. 203, 173-179.
34. Bairoch, A., and Apweiler, R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48.
35. Clauser, K. R., Baker, P., and Burlingame, A. L. (1999) Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882.
36. Gatlin, C. L., Kleemann, G. R., Hays, L. G., Link, A. J., and Yates, J. R., III. (1998) Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. Anal. Biochem. 263, 93-101.
37. Guex, N., and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714-2723.
38. Phillips, D. M. (1968) N-Terminal acetyl-peptides from two calf thymus histones. Biochem. J. 107, 135-138.
39. Candido, E. P., and Dixon, G. H. (1971) Sites of in vivo acetylation in trout testis histone IV. J. Biol. Chem. 246, 3182-3188.
40. Yu, T., Wang, X., Purring-Koch, C., Wei, Y., and McLendon, G. L. (2001) A mutational epitope for cytochrome C binding to the apoptosis protease activation factor-1. J. Biol. Chem. 276, 13034-13038.