New and automated MSn approaches for top-down identification of modified proteins

Journal of the American Society for Mass Spectrometry

Volumn 16, Issue 12, 2005, Pages 2027-2038

  Zabrouskov, Vlad ^a   Senko, Michael W ^a   Du, Yi ^b   Leduc, Richard D ^b   Kelleher, Neil L ^b  

^a Thermo Fisher Scientific   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DATABASE SYSTEMS; DISSOCIATION; FOURIER TRANSFORMS; LIQUID CHROMATOGRAPHY; PROTEINS; YEAST;

AMINO ACID SEQUENCES; CHARGE STATE; LINEAR ION TRAP (LIP); MOLECULAR IONS;

MASS SPECTROMETERS;

FUNGAL PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; AUTOANALYZER; DISSOCIATION; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MASS SPECTROMETRY; PHASE SEPARATION; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEIN PROCESSING; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SEPARATION TECHNIQUE; WILD TYPE; ELECTROSPRAY MASS SPECTROMETRY; EVALUATION; INFRARED SPECTROSCOPY; LIQUID CHROMATOGRAPHY; METHODOLOGY; MOLECULAR GENETICS; ONLINE SYSTEM; PEPTIDE MAPPING; ROBOTICS; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; CHROMATOGRAPHY, LIQUID; MOLECULAR SEQUENCE DATA; ONLINE SYSTEMS; PEPTIDE MAPPING; ROBOTICS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 27844511528     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2005.08.004     Document Type: Article

References (30)

1. W.J. Henzel, T.M. Billeci, J.T. Stults, S.C. Wong, C. Grimley, C. Watanabe Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases Proc. Natl. Acad. Sci. U.S.A. 90 1993 5011 5015
2. J.R. Yates III,.E. Carmack,.L. Hays,.A.J. Link,.J.K. Eng Automated protein identification using microcolumn liquid chromatography-tandem mass spectrometry Methods Mol. Biol. 112 1999 553 569
3. G.E. Reid, S.A. McLuckey Top down protein characterization via tandem mass spectrometry J. Mass Spectrom. 37 2002 663 675
4. N.L. Kelleher Top down proteomics Anal. Chem. 76 2004 197A 203A
5. G.E. Reid, J.L. Stephenson, S.A. McLuckey Tandem mass spectrometry of ribonuclease A and B N-linked glycosylation site analysis of whole protein ions Anal. Chem 74 2002 577 583
6. F. Meng, B.J. Cargile, L.M. Miller, A.J. Forbes, J.R. Johnson, N.L. Kelleher Informatics and multiplexing of intact protein identification in bacteria and the archaea Nat. Biotech. 19 2001 952 957
7. T. Baba, Y. Hashimoto, H. Hasegawa, A. Hirabayashi, I. Waki Electron capture dissociation in a radio frequency ion trap Anal. Chem. 76 2004 4263 4266
8. J.M. Ginter, F. Zhou, M.V. Johnston Generating protein sequence tags by combining cone and conventional collision induced dissociation in a quadrupole time-of-flight mass spectrometer J. Am. Soc. Mass Spectrom. 15 2004 1478 1486
9. J.F. Nemeth-Cawley, B.S. Tangarone, J.C. Rouse "Top Down" characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures J. Proteome Res. 2 2003 495 505
10. R. Amunugama, J.M. Hogan, K.A. Newton, S.A. McLuckey Whole protein dissociation in a quadrupole ion trap Identification of an a priori unknown modified protein Anal. Chem. 76 2004 720 727
11. M.W. Senko, J.P. Speir, F.W. McLafferty Collisional activation of large multiply charged ions using Fourier transform mass spectrometry Anal. Chem. 66 1994 2801 2808
12. E. Mortz,.P.B. O'Connor, P. Roepstorff, N.L. Kelleher, T.D. Wood, F.W. McLafferty, M. Mann Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases Proc. Natl. Acad. Sci. U.S.A. 93 1996 8264 8267
13. F. Meng, Y. Du, L.M. Miller, S.M. Patrie, D.E. Robinson, N.L. Kelleher Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics Anal. Chem 76 2004 2852 2858
14. G.K. Taylor, Y.B. Kim, A.J. Forbes, F. Meng, R. McCarthy, N.L. Kelleher Web and database software for identification of intact proteins using "top down" mass spectrometry Anal. Chem. 75 2003 4081 4086
15. R.D. LeDuc, G.K. Taylor, Y.B. Kim, T.E. Januszyk, L.H. Bynum, J.V. Sola, J.S. Garavelli, N.L. Kelleher ProSight PTM an integrated environment for protein identification and characterization by top-down mass spectrometry Nucleic Acids Res. 32 2004 W340 W345
16. J.J. Pesavento, Y.B. Kim, G.K. Taylor, N.L. Kelleher Shotgun annotation of histone modifications a new approach for streamlined characterization of proteins by top down mass spectrometry J. Am. Chem. Soc. 126 2004 4081 4086
17. R.A. Zubarev, N.L. Kelleher, F.W. McLafferty Electron capture dissociation of multiply charged protein cations. A nonergodic process J. Am. Chem. Soc. 120 1998 3265 3266
18. R.A. Zubarev, N.A. Kruger, E.K. Fridriksson, M.A. Lewis, D.M. Horn, B.K. Carpenter, F.W. McLafferty Electron capture dissociation of gaseous multiply-charged proteins is favored at disulfide bonds and other sites of high hydrogen atom affinity J. Am. Chem. Soc. 121 1999 2857 2862
19. R.A. Zubarev, D.M. Horn, E.K. Fridriksson, N.L. Kelleher, N.A. Kruger, M.A. Lewis, B.K. Carpenter, F.W. McLafferty Electron capture dissociation for structural characterization of multiply charged protein cations Anal. Chem. 72 2000 563 573
20. S.K. Sze, Y. Ge, H. Oh, F.W. McLafferty Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry Anal. Chem. 75 2003 1599 1603
21. S.K. Sze, Y. Ge, H. Oh, F.W. McLafferty Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue Proc. Natl. Acad. Sci. U.S.A. 99 2002 1774 1779
22. Y. Ge, M. El-Naggar, S.K. Sze, H.B. Oh, T.P. Begley, F.W. McLafferty, H. Boshoff, C.E. Barry Top down characterization of secreted proteins from Mycobacterium tuberculosis by electron capture dissociation mass spectrometry J. Am. Soc. Mass Spectrom. 14 2003 253 261
23. J.E. Syka, J.J. Coon, M.J. Schroeder, J. Shabanowitz, D.F. Hunt Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 101 2004 9528 9533
24. S.L. Wu, I. Jardine, W.S. Hancock, B.L. Karger A new and sensitive on-line liquid chromatography/mass spectrometric approach for top-down protein analysis The comprehensive analysis of human growth hormone in an E. coli lysate using a hybrid linear ion trap/Fourier transform ion cyclotron resonance mass spectrometer Rapid Commun. Mass Spectrom 18 2004 2201 2207
25. M.B. Strader, N.C. Verberkmoes, D.L. Tabb, H.M. Connelly, J.W. Barton, B.D. Bruce, D.A. Pelletier, B.H. Davison, R.L. Hettich, F.W. Larimer, G.B. Hurst Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach J. Proteome Res. 3 2004 965 978
26. Y. Du, F. Meng, S.M. Patrie, L.M. Miller, N.L. Kelleher Improved molecular weight-based processing of intact proteins for interrogation by quadrupole-enhanced FT MS/MS J. Proteome Res. 3 2004 801 806
27. J.V. Olsen, M. Mann Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation Proc. Natl. Acad. Sci. U.S.A. 101 2004 13417 13422
28. LeDuc, R. D.; Roth, M. J.; Boyne, M. T., II; Kim, Y.; Forbes, A. J.; Kelleher N. L. The bioinformatics of human top down proteomics. Proceedings of the 53rd Annual Meeting of the American Society for Mass Spectrometry; San Antonio, TX, June 2005.
29. S.M. Patrie, J.P. Charlebois, D. Whipple, N.L. Kelleher, C.L. Hendrickson, J.P. Quinn, A.G. Marshall, B. Mukhopadhyay Construction of a hybrid quadrupole/Fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa J. Am. Soc. Mass Spectrom. 15 2004 1099 1108
30. J.J. Coon, B. Ueberheide, J.E. Syka, D.D. Dryhurst, J. Ausio, J. Shabanowitz, D.F. Hunt Protein identification using sequential ion/ion reactions and tandem mass spectrometry Proc. Natl. Acad. Sci. U. S. A. 102 2005 9463 9468