Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS

FEBS Journal

Volumn 274, Issue 24, 2007, Pages 6269-6276

  Udeshi, Namrata D ^a   Shabanowitz, Jeffrey ^a   Hunt, Donald F ^a,b   Rose, Kristie L ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Cell migration; Chromatin; HIV regulator of expression of virion products; Mass spectrometry; O GlcNAcylation; Phosphorylation; Post translational modifications; Protein identification

Indexed keywords

AMIDE; FLUORANTHENE; PEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; CHROMATOGRAPHY; ELECTRON TRANSPORT; FRAGMENTATION REACTION; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; SHORT SURVEY;

AMINO ACID SEQUENCE; CHROMATOGRAPHY, LIQUID; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PEPTIDES; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 36749094051     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2007.06148.x     Document Type: Short Survey

References (34)

1. Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG Hunt DF (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA 104, 2193 2198.
2. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF White FM (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20, 301 305.
3. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101, 9528 9533.
4. Mikesh LM, Ueberheide B, Chi A, Coon JJ, Syka JE, Shabanowitz J Hunt DF (2006) The utility of ETD mass spectrometry in proteomic analysis. Biochim Biophys Acta 1764, 1811 1822.
5. Zubarev RA, Kelleher NL McLafferty FW (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. J Am Chem Soc 120, 3265 3266.
6. Han X, Jin M, Breuker K McLafferty FW (2006) Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 314, 109 112.
7. McLafferty FW, Breuker K, Jin M, Han X, Infusini G, Jiang H, Kong X Begley T (2007) Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J 274, doi :
8. Coon JJ, Ueberheide B, Syka JEP, Dryhurst DD, Ausio J, Shabanowitz J Hunt DF (2005) Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci USA 102, 9463 9468.
9. Turner CE (2000) Paxillin and focal adhesion signalling. Nat Cell Biol 2, E231 E236.
10. Schroeder MJ, Webb DJ, Shabanowitz J, Horwitz AF Hunt DF (2005) Methods for the detection of paxillin post-translational modifications and interacting proteins by mass spectrometry. J Proteome Res 4, 1832 1841.
11. Torres CR Hart GW (1984) Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc. J Biol Chem 259, 3308 3317.
12. Hart GW, Housley MP Slawson C (2007) Cycling of O-linked [beta]-N-acetylglucosamine on nucleocytoplasmic proteins. Nature 446, 1017 1022.
13. Wells L, Vosseller K Hart GW (2001) Glycosylation of nucleocytoplasmic proteins: signal transduction and O-GlcNAc. Science 291, 2376 2378.
14. Taverna SD, Ueberheide BM, Liu Y, Tackett AJ, Diaz RL, Shabanowitz J, Chait BT, Hunt DF Allis CD (2007) Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini. Proc Natl Acad Sci USA 104, 2086 2091.
15. Luger K Richmond TJ (1998) The histone tails of the nucleosome. Curr Opin Genet Dev 8, 140 146.
16. Garcia BA, Barber CM, Hake SB, Ptak C, Turner FB, Busby SA, Shabanowitz J, Moran RG, Allis CD Hunt DF (2005) Modifications of human histone H3 variants during mitosis. Biochemistry 44, 13202 13213.
17. Zhang Y (2003) Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev 17, 2733 2740.
18. Strahl BD Allis CD (2000) The language of covalent histone modifications. Nature 403, 41 45.
19. Jenuwein T Allis CD (2001) Translating the histone code. Science 293, 1074 1080.
20. Stephenson JL McLuckey SA (1996) Ion/ion reactions in the gas phase. Proton transfer reactions involving multiply-charged proteins. J Am Chem Soc 118, 7390 7397.
21. Chi A, Bai DL, Geer LY, Shabanowitz J Hunt DF (2007) Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. Int J Mass Spectrom 259, 197 203.
22. Ramakrishnan V White SW (1998) Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends Biochem Sci 23, 208 212.
23. Pollard VW Malim MH (1998) The HIV-1 Rev protein. Annu Rev Microbiol 52, 491 532.
24. Hammarskjold ML (1997) Regulation of retroviral RNA export. Semin Cell Dev Biol 8, 83 90.
25. Liang X, Xia Y McLuckey SA (2006) Alternately pulsed nanoelectrospray ionization/atmospheric pressure chemical ionization for ion/ion reactions in an electrodynamic ion trap. Anal Chem 78, 3208 3212.
26. Montgomery HA, Blakeslee J, DeLong A, Shabanowitz J Hunt DF (2007) Arabidopsis thaliana phosphopeptide identification by electron transfer dissociation mass spectrometry. In Proteomics: Phosphorylation. Proceedings of the 55th ASMS Conference on Mass Spectrometry and Allied Topics, Indianapolis, IN.
27. McAlister G, Makarov A, Horning S, Schwartz JC, Phanstiel D, Good D, Berggren WT Coon JJ (2007) Implementation of electron transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. In Developments in Ion Trap MS. Proceedings of the 55th ASMS Conference on Mass Spectrometry and Allied Topics, Indianapolis, IN.
28. McAlister GC, Phanstiel D, Good DM, Berggren WT Coon JJ (2007) Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal Chem 79, 3525 3534.
29. Udeshi ND, Misawa Y, Lindsey Rose KM, Chi A, Rekosh D, Shabanowitz J, Hammarskjold M Hunt DF (2007) A sensitive top down and middle down strategy for analyzing proteins using electron transfer dissociation. In Top Down 2007: Tandem MS Above 5 kDa. Proceedings of the 55th ASMS Conference on Mass Spectrometry and Allied Topics, Indianapolis, IN.
30. Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JEP Coon JJ (2007) Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem 79, 477 485.
31. Molina H, Horn DM, Tang N, Mathivanan S Pandey A (2007) Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci USA 104, 2199 2204.
32. Good DM, Wirtala M, McAlister GC Coon JJ (2007) Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics, in press.
33. Zhang Q, Frolov A, Tang N, Hoffmann R, van de Goor T, Metz TO Smith RD (2007) Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides. Rapid Commun Mass Spectrom 21, 661 666.
34. Catalina MI, Koeleman CA, Deelder AM Wuhrer M (2007) Electron transfer dissociation of N-glycopeptides: loss of the entire N-glycosylated asparagine side chain. Rapid Commun Mass Spectrom 21, 1053 1061.