Application of the ETD/PTR reactions in top-down proteomics as a faster alternative to bottom-up nanoLC-MS/MS protein identification

Journal of Mass Spectrometry

Volumn 47, Issue 10, 2012, Pages 1347-1352

  Drabik, A ^a   Bodzon Kulakowska, A ^a   Suder, P ^a  

^a AGH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Poland)

Author keywords

electron transfer dissociation; nanoLC MS MS; protein identification; proteomics; proton transfer reaction

Indexed keywords

ELECTRON TRANSFER DISSOCIATION; NANOLC-MS/MS; PROTEIN IDENTIFICATION; PROTEOMICS; PROTON TRANSFER REACTIONS;

CHARGE TRANSFER; DISSOCIATION; ELECTRON TRANSITIONS; PROTEINS;

MOLECULAR BIOLOGY;

DYNORPHIN A; LYSOZYME; MYOGLOBIN; NEUROPEPTIDE Y; PEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; DISSOCIATION; ELECTRON TRANSFER DISSOCIATION; ELECTRON TRANSPORT; ELECTROSPRAY MASS SPECTROMETRY; ION TRAP MASS SPECTROMETRY; LIQUID CHROMATOGRAPHY; MOLECULAR WEIGHT; NANO LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEOMICS; PROTON TRANSFER REACTION; PROTON TRANSPORT; REACTION TIME; TANDEM MASS SPECTROMETRY; TIME SERIES ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; CHROMATOGRAPHY, LIQUID; MASS SPECTROMETRY; METHANOL; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PEPTIDES; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; TANDEM MASS SPECTROMETRY;

EID: 84867009703     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.3086     Document Type: Article

References (19)

1. P. Dittwald, J. Ostrowski, J. Kaczmarski, A. Gambin,. Interferring serum proteolytic activity from LC-MS/MS data. BMC Bioinformatics 2012, 13 (suppl 5), S7.
2. A. Michalski, E. Damoc, O. Lange, E. Denisov, D. Nolting, M. Muller, R. Viner, J. Schwartz, P. Remes, M. Belford, J. J. Dunyach, J. Cox, S. Horning, M. Mann, A. Makarov,. Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 2012, 11 (3), O111.013698.
3. L. M. Mikesh, B. Ueberheide, A. Chi, J. J. Coon, J. E. Syka, J. Shabanowitz, D. F. Hunt,. The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta 2006, 1764 (12), 1811.
4. R. A. Zubarev, A. R. Zubarev, M. M. Savitski,. Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet?. J. Am. Soc. Mass Spectrom. 2008, 19 (6), 753.
5. A. Guthals, N. Bandeira,. Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol. Cell. Proteomics 2012, DOI 10.1074/MCP.R112.018556
6. M. S. Kim, A. Pandey,. Electron transfer dissociation mass spectrometry in proteomics. Proteomics 2012, 12 (4-5), 530.
7. S. L. Wu, A. F. Huhmer, Z. Hao, B. L. Karger,. On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD) and CID of an isolated charge reduced species for the trace-level characterization of proteins with post-translational modifications. J. Proteome Res. 2007, 6 (11), 4230.
8. C. Smet-Nocca, C. M. Broncel, J. M. Wieruszeski, C. Tokarski, X. Hanoulle, A. Leroy, I. Landrieu, C. Rolando, G. Lippens, C. P. Hackenberger,. Identification of O-GlcNAc sites within peptides of the Tau protein and their impact on phosphorylation. Mol. Biosyst. 2011, 7 (5), 1420.
9. A. Chi, D. L. Bai, L. Y. Geer, J. Shabanowitz, D. F. Hunt,. Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. Int. J. Mass Spectrom. 2007, 259 (1-3), 197.
10. H. P. Gunawardena, M. He, P. A. Chrisman, S. J. Pitteri, J. M. Hogan, B. D. M. Hodges, S. A. McLuckey,. Electron transfer versus proton transfer in gas phase ion/ion reactions of polyprotonated peptides. J. Am. Chem. Soc., 2005, 127 (36), 12627.
11. P. Suder, A. Bodzon-Kulakowska, P. Mak, A. Bierczynska-Krzysik, M. Daszykowski, B. Walczak, G. Lubec, J. H. Kotlinska, J. Silberring,. The proteomic analysis of primary cortical astrocyte cell culture after morphine administration. J. Proteome Res. 2009, 8 (10), 4633.
12. A. Shevchenko, M. Wilm, O. Vorm, M. Mann,. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 1996, 68 (5), 850.
13. J. Havlis, H. Thomas, M. Sebela, A. Shevchenko,. Fast-response proteomics by accelerated in-gel digestion of proteins. Anal. Chem. 2003, 75 (6), 1300.
14. A. Alam, A. Mataj, Y. Yang, R. I. Boysen, D. K. Bowden, M. T. Hearn,. Rapid microwave-assisted chemical cleavage-mass spectrometric method for the identification of hemoglobin variants in blood. Anal. Chem. 2010, 82 (21), 8922.
15. F. Dycka, P. Bobal, K. Mazanec, J. Bobalova,. Rapid and efficient protein enzymatic digestion: an experimental comparison. Electrophoresis 2012, 33, 288.
16. S. R. Hart,. A protocol for top-down proteomics using HPLC and ETD/PTR-MS. Methods Mol. Biol. 2010, 658, 339-353.
17. C. A. Retamal, P. Thiebaut, E. W. Alves,. Protein purification from polyacrylamide gels by sonication extraction. Anal. Biochem. 1999, 268, 15.
18. B. T. Kurien, R. H. Scofield,. Extraction of proteins from gels: a brief review. Methods Mol. Biol. 2012, 869, 403.
19. S. Bornemann, B. Rietschel, S. Baltruschat, M. Karas, B. Meyer,. A novel polyacrylamide gel system for proteomic use offering controllabel pore expansion by crosslinker cleavage. Electrophoresis 2010, 31 (4), 585.