Characterization of green fluorescent proteins by 193 nm ultraviolet photodissociation mass spectrometry

Proteomics

Volumn 14, Issue 10, 2014, Pages 1165-1173

  Cannon, Joe R ^a   Kluwe, Christien ^b   Ellington, Andrew ^b   Brodbelt, Jennifer S ^a  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Green fluorescent protein; Orbitrap; Technology; Top down; Ultraviolet photodissociation

Indexed keywords

GREEN FLUORESCENT PROTEIN; PEPTIDE FRAGMENT;

ARTICLE; MASS SPECTROMETRY; POINT MUTATION; PRIORITY JOURNAL; SURFACE CHARGE; SURFACE PROPERTY; TANDEM MASS SPECTROMETRY; ULTRAVIOLET PHOTODISSOCIATION MASS SPECTROMETRY; CHEMISTRY; PROCEDURES; PROTEOMICS; ULTRAVIOLET RADIATION; COMPARATIVE STUDY; ELECTRON TRANSFER DISSOCIATION; ELECTRON TRANSPORT; INVESTIGATIVE PROCEDURES; ULTRAVIOLET PHOTODISSOCIATION;

GREEN FLUORESCENT PROTEINS; PEPTIDE FRAGMENTS; PROTEOMICS; TANDEM MASS SPECTROMETRY; ULTRAVIOLET RAYS;

EID: 84899822392     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300364     Document Type: Article

References (33)

1. Geiger, T., Velic, A., Macek, B., Lundberg, E. et al., Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol. Cell. Proteomics 2013, 12, 1709-1722.
2. Kim, W., Bennett, E. J., Huttlin, E. L., Guo, A. et al., Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 2011, 44, 325-340.
3. Li, W., Ji, L., Goya, J., Tan, G., Wysocki, V. H., SQID: An intensity-incorporated protein identification algorithm for tandem mass spectrometry. J. Proteome Res. 2011, 10, 1593-1602.
4. Hansen, T. A., Kryuchkov, F., Kjeldsen, F., Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra. Anal. Chem. 2012, 84, 6638-6645.
5. Wu, S.-L., Kim, J., Hancock, W. S., Karger, B., Extended range proteomic analysis (erpa): a new and sensitive lc-ms platform for high sequence coverage of complex proteins with extensive post-translational modificationscomprehensive analysis of beta-casein and epidermal growth factor receptor (egfr)†. J. Proteome Res. 2005, 4, 1155-1170.
6. Cannon, J., Lohnes, K., Wynne, C., Wang, Y. et al., High-throughput middle-down analysis using an orbitrap. J. Proteome Res. 2010, 9, 3886-3890.
7. Wu, C., Tran, J.C., Zamdborg, L., Durbin, K. R. et al., A protease for "middle-down" proteomics. Nat. Meth. 2012, 9, 822-824.
8. Yergey, J. A., Cotter, R. J., Heller, D., Fenselau, C., Resolution requirements for middle molecule mass spectrometry. Anal. Chem. 1984, 56, 2262-2263.
9. Young, N. L., Plazas-Mayorca, M. D., DiMaggio, P. A., Flaniken, I. Z. et al., Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a. J. Am. Soc. Mass Spectrom. 2010, 21, 960-970.
10. Boyne, M. T., Garcia, B. A., Li, M., Zamdborg, L. et al., Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval. J. Proteome Res. 2008, 8, 374-379.
11. Compton, P. D., Zamdborg, L., Thomas, P. M., Kelleher, N. L., On the Scalability and Requirements of Whole Protein Mass Spectrometry. Anal. Chem. 2011, 83, 6868-6874.
12. Mørtz, E., O'Connor, P. B., Roepstorff, P., Kelleher, N. L. et al., Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. 1996, 93, 8264-8267.
13. Liu, Z., Schey, K. L., Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry. J. Am. Soc. Mass Spectrom. 2008, 19, 231-238.
14. Wysocki, V. H., Tsaprailis, G., Smith, L. L., Breci, L. A., Mobile and localized protons: a framework for understanding peptide dissociation. J. Mass Spectrom. 2000, 35, 1399-1406.
15. Chanthamontri, C., Liu, J., McLuckey, S. A., Charge state dependent fragmentation of gaseous α-synuclein cations via ion trap and beam-type collisional activation. Int. J. Mass Spectrom. 2009, 283, 9-16.
16. Zubarev, R. A., Kelleher, N. L., McLafferty, F. W., Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process. J. Am. Chem. Soc. 1998, 120, 3265-3266.
17. Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., Hunt, D. F., Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 9528-9533.
18. Good, D. M., Wirtala, M., McAlister, G. C., Coon, J. J., Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteomics 2007, 6, 1942-1951.
19. Wynne, C., Edwards, N. J., Fenselau, C., Phyloproteomic classification of unsequenced organisms by top-down identification of bacterial proteins using capLC-MS/MS on an Orbitrap. Proteomics 2010, 10, 3631-3643.
20. Shaw, J. B., Li, W., Holden, D. D., Zhang, Y. et al., Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation. J. Am. Chem. Soc. 2013, 135, 12646-12651.
21. Thompson, M. S., Cui, W., Reilly, J. P., Factors that impact the vacuum ultraviolet photofragmentation of peptide ions. J. Am. Soc. Mass Spectrom. 2007, 18, 1439-1452.
22. Madsen, J. A., Boutz, D. R., Brodbelt, J. S., Ultrafast ultraviolet photodissociation at 193 nm and its applicability to proteomic workflows. J. Proteome Res. 2010, 9, 4205-4214.
23. Moon, J. H., Shin, Y. S., Cha, H. J., Kim, M. S., Photodissociation at 193 nm of some singly protonated peptides and proteins with m/z 2000-9000 using a tandem time-of-flight mass spectrometer equipped with a second source for delayed extraction/post-acceleration of product ions. Rapid Commun. Mass Spectrom. 2007, 21, 359-368.
24. Reilly, J. P., Ultraviolet photofragmentation of biomolecular ions. Mass Spectrom. Rev. 2009, 28, 425-447.
25. Parthasarathi, R., He, Y., Reilly, J. P., Raghavachari, K., New insights into the vacuum UV photodissociation of peptides. J. Am. Chem. Soc. 2010, 132, 1606-1610.
26. Guan, Z., Kelleher, N. L., O'Connor, P. B., Aaserud, D. J. et al., 193 nm photodissociation of larger multiply-charged biomolecules. Int. J. Mass Spectrom. Ion Process. 1996, 157, 357-364.
27. Kim, T.-Y., Thompson, M. S., Reilly, J. P., Peptide photodissociation at 157 nm in a linear ion trap mass spectrometer. Rapid Commun. Mass Spectrom. 2005, 19, 1657-1665.
28. Der, B. S., Kluwe, C., Miklos, A. E., Jacak, R. et al., Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. PLoS ONE 2013, 8, e64363.
29. Tsien, R. Y., The green fluorescent protein. Annu. Rev. Biochem. 1998, 67, 509-544.
30. Vasicek, L. A., Ledvina, A. R., Shaw, J., Griep-Raming, J. et al., Implementing photodissociation in an orbitrap mass spectrometer. J. Am. Soc. Mass Spectrom. 2011, 22, 1105-1108.
31. Makarov, A., Denisov, E., Dynamics of ions of intact proteins in the Orbitrap mass analyzer. J. Am. Soc. Mass Spectrom. 2009, 20, 1486-1495.
32. Horn, D. M., Zubarev, R. A., McLafferty, F. W., Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.
33. Chi, A., Bai, D. L., Geer, L. Y., Shabanowitz, J., Hunt, D. F., Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry. Int. J. Mass Spectrom. 2007, 259, 197-203.