Systematic comparison of ultraviolet photodissociation and electron transfer dissociation for peptide anion characterization

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 10, 2012, Pages 1707-1715

  Shaw, Jared B ^a   Madsen, James A ^a   Xu, Hua ^b   Brodbelt, Jennifer S ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Negative electron transfer dissociation; Protein identification; Tandem mass spectrometry; Ultraviolet photodissociation

Indexed keywords

CHARGE STATE; CHARGED SPECIES; CLEAVAGE PREFERENCE; COVERAGE PERCENTAGE; DATABASE SEARCHING; DIAGNOSTIC INFORMATION; ELECTRON TRANSFER DISSOCIATION; HETEROGENEOUS ARRAY; HIGH PH; ION SIGNALS; MOBILE PHASIS; PEPTIDE ANIONS; PEPTIDE BACKBONES; PEPTIDE IDENTIFICATION; POSITIVE MODE; PROTEIN DIGESTS; PROTEIN IDENTIFICATION; PROTEOMES; RAPID ACTIVATION; TANDEM MASS SPECTROMETRY; ULTRAVIOLET PHOTODISSOCIATION;

CHEMICAL REACTIONS; ELECTRON TRANSITIONS; MASS SPECTROMETRY; PEPTIDES; PHOTODISSOCIATION; SEARCH ENGINES;

IONS;

ACID PROTEIN; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; AUTOANALYSIS; COLLISIONALLY ACTIVATED DISSOCIATION; CONTROLLED STUDY; DISSOCIATION; ELECTRON TRANSPORT; FRAGMENTATION REACTION; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NEGATIVE ELECTRON TRANSFER DISSOCIATION; PEPTIDE ANALYSIS; PH; PHYSICAL PHASE; REACTION TIME; SEQUENCE DATABASE; SIGNAL DETECTION; STRUCTURAL PROTEOMICS; SURFACE CHARGE; TANDEM MASS SPECTROMETRY; ULTRAVIOLET PHOTODISSOCIATION; ULTRAVIOLET RADIATION;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ANIONS; CATTLE; CHICKENS; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PEPTIDES; PHOTOLYSIS; PROTEINS; TANDEM MASS SPECTROMETRY; ULTRAVIOLET RAYS;

EID: 84868235717     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0424-9     Document Type: Article

References (50)

1. Hunt, D.F., Buko, A.M., Ballard, J.M., Shabanowitz, J., Giordani, A.B.: Sequence analysis of polypeptides by collision activated dissociation on a triple quadrupole mass spectrometer. Biol. Mass Spectrom. 8, 397-408 (1981)
2. McLuckey, S.: Principles of collisional activation in analytical mass spectrometry. J. Am. Soc. Mass Spectrom. 3, 599-614 (1992)
3. Eng, J.K., McCormack, A.L., Yates III, J.R.: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994)
4. Perkins, D.N., Pappin, D.J.C., Creasy, D.M., Cottrell, J.S.: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999)
5. de Godoy, L.M.F., Olsen, J.V., Cox, J., Nielsen, M.L., Hubner, N.C., Frohlich, F., Walther, T.C., Mann, M.: Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008)
6. Zubarev, R.A., Kelleher, N.L., McLafferty, F.W.: Electron capture dissociation of multiply charged protein cations. A nonergodic process. J. Am. Chem. Soc. 120, 3265-3266 (1998)
7. Kelleher, N.L., Zubarev, R.A., Bush, K., Furie, B., Furie, B.C., McLafferty, F.W., Walsh, C.T.: Localization of labile post-translational modifications by electron capture dissociation: the case of γ- carboxyglutamic acid. Anal. Chem. 71, 4250-4253 (1999)
8. Zubarev, R.A., Horn, D.M., Fridriksson, E.K., Kelleher, N.L., Kruger, N.A., Lewis, M.A., Carpenter, B.K., McLafferty, F.W.: Electron capture dissociation for structural characterization of multiply charged protein cations. Anal. Chem. 72, 563-573 (2000)
9. 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. PNAS 101, 9528-9533 (2004)
10. Coon, J.J., Syka, J.E.P., Schwartz, J.C., Shabanowitz, J., Hunt, D.F.: Anion dependence in the partitioning between proton and electron transfer in ion/ion reactions. Int. J. Mass Spectrom. 236, 33-42 (2004)
11. Good, D.M., Wirtala, M., McAlister, G.C., Coon, J.J.: Performance characteristics of electron transfer dissociation mass spectrometry. Mol. Cell. Proteom. 6, 1942-1951 (2007)
12. Bowers, W.D., Delbert, S.S., Hunter, R.L., McIver, R.T.: Fragmentation of oligopeptide ions using ultraviolet laser radiation and Fourier transform mass spectrometry. J. Am. Chem. Soc. 106, 7288-7289 (1984)
13. Little, D.P., Speir, J.P., Senko, M.W., O'Connor, P.B., McLafferty, F.W.: Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Anal. Chem. 66, 2809-2815 (1994)
14. Hofstadler, S.A., Sannes-Lowery, K.A., Griffey, R.H.: Infrared multiphoton dissociation in an external ion reservoir. Anal. Chem. 71, 2067-2070 (1999)
15. Wilson, J.J., Brodbelt, J.S.: Infrared multiphoton dissociation for enhanced de novo sequence interpretation of N-terminal sulfonated peptides in a quadrupole ion trap. Anal. Chem. 78, 6855-6862 (2006)
16. Morgan, J.W., Hettick, J.M., Russell, D.H.: In: Biological Mass Spectrometry; Academic Press; Vol. 402, pp. 186-209 (2005)
17. 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. 19, 1657-1665 (2005)
18. Ly, T., Julian, R.R.: Ultraviolet photodissociation: developments towards applications for mass-spectrometry-based proteomics. Angew. Chem. Int. Ed. 48, 7130-7137 (2009)
19. Reilly, J.P.: Ultraviolet photofragmentation of biomolecular ions. Mass Spectrom. Rev. 28, 425-447 (2009)
20. Ly, T., Julian, R.R.: Residue-specific radical-directed dissociation of whole proteins in the gas phase. J. Am. Chem. Soc. 130, 351-358 (2008)
21. Morgan, J.W., Russell, D.H.: Comparative studies of 193-nm photodissociation and TOF-TOFMS analysis of bradykinin analogues: the effects of charge site(s) and fragmentation timescales. J. Am. Soc. Mass Spectrom. 17, 721-729 (2006)
22. Thompson, M.S., Cui, W., Reilly, J.P.: Factors that impact the vacuum ultraviolet photofragmentation of peptide ions. J. Am. Soc. Mass Spectrom. 18, 1439-1452 (2007)
23. Kim, T.-Y., Reilly, J.P.: Time-resolved observation of product ions generated by 157 nm photodissociation of singly protonated phosphopeptides. J. Am. Soc. Mass Spectrom. 20, 2334-2341 (2009)
24. Madsen, J.A., Boutz, D.R., Brodbelt, J.S.: Ultrafast ultraviolet photodissociation at 193 nm and its applicability to proteomic workflows. J. Proteome Res. 9, 4205-4214 (2010)
25. Shin, Y.S., Moon, J.H., Kim, M.S.: Observation of phosphorylation site-specific dissociation of singly protonated phosphopeptides. J. Am. Soc. Mass Spectrom. 21, 53-59 (2010)
26. Brodbelt, J.S.: Shedding light on the frontier of photodissociation. J. Am. Soc. Mass Spectrom. 22, 197-206 (2001)
27. Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: a statistical interpretation. J. Am. Soc. Mass Spectrom. 19, 645-655 (2008)
28. Janek, K., Wenschuh, H., Bienert, M., Krause, E.: Phosphopeptide analysis by positive and negative ion matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 15, 1593-1599 (2001)
29. Gunawardena, H.P., Emory, J.F., McLuckey, S.A.: Phosphopeptide anion characterization via sequential charge inversion and electron-transfer dissociation. Anal. Chem. 78, 3788-3793 (2006)
30. Ewing, N., Cassady, C.: Dissociation of multiply charged negative ions for hirudin (54-65), fibrinopeptide B, and insulin A (oxidized). J. Am. Soc. Mass Spectrom. 12, 105-116 (2001)
31. - parent anions of underivatized peptides: An aid to structure determination and some unusual negative ion cleavages. Mass Spectrom. Rev. 21, 87-107 (2002)
32. - ions derived from caeridin and dynastin peptides. Internal backbone cleavages directed through Asp and Asn residues. Rapid Commun. Mass Spectrom. 11, 253-258 (1997)
33. Jensen, O.N.: Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell. Biol. 7, 391-403 (2006)
34. Schwartz, R., Ting, C.S., King, J.: Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. Genome Res. 11, 703-709 (2001)
35. Knight, C.G., Kassen, R., Hebestreit, H., Rainey, P.B.: Global analysis of predicted proteomes: functional adaptation of physical properties. Proc. Nat. Acad. Sci. U.S.A. 101, 8390-8395 (2004)
36. Weiller, G.F., Caraux, G., Sylvester, N.: The modal distribution of protein isoelectric points reflects amino acid properties rather than sequence evolution. Proteomics 4, 943-949 (2004)
37. Kiraga, J., Mackiewicz, P., Mackiewicz, D., Kowalczuk, M., Biecek, P., Polak, N., Smolarczyk, K., Dudek, M., Cebrat, S.: The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. BMC Genom. 8, 163 (2007)
38. Kjeldsen, F., Silivra, O.A., Ivonin, I.A., Haselmann, K.F., Gorshkov, M., Zubarev, R.A.: Cα-C Backbone Fragmentation Dominates in Electron Detachment Dissociation of Gas-Phase Polypeptide Polyanions. Chem. Eur. J. 11, 1803-1812 (2005)
39. Kjeldsen, F., Horning, O.B., Jensen, S.S., Giessing, A.M.B., Jensen, O.N.: Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negativeion mode using electron detachment dissociation tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 1156-1162 (2008)
40. Larraillet, V., Vorobyev, A., Brunet, C., Lemoine, J., Tsybin, Y.O., Antoine, R., Dugourd, P.: Comparative dissociation of peptide polyanions by electron impact and photo-induced electron detachment. J. Am. Soc. Mass Spectrom. 21, 670-680 (2010)
41. Cook, S., Jackson, G.: Metastable atom-activated dissociation mass spectrometry of phosphorylated and sulfonated peptides in negative ion mode. J. Am. Soc. Mass Spectrom. 22, 1088-1099 (2011)
42. Huzarska, M., Ugalde, I., Kaplan, D.A., Hartmer, R., Easterling, M.L., Polfer, N.C.: Negative electron transfer dissociation of deprotonated phosphopeptide anions: choice of radical cation reagent and competition between electron and proton transfer. Anal. Chem. 82, 2873-2878 (2010)
43. Coon, J.J., Shabanowitz, J., Hunt, D.F., Syka, J.E.P.: Electron transfer dissociation of peptide anions. J. Am. Soc. Mass Spectrom. 16, 880-882 (2005)
44. Madsen, J.A., Kaoud, T.S., Dalby, K.N., Brodbelt, J.S.: 193-nm photodissociation of singly and multiply charged peptide anions for acidic proteome characterization. Proteomics 11, 1329-1334 (2011)
45. Antoine, R., Joly, L., Tabarin, T., Broyer, M., Dugourd, P., Lemoine, J.: Photo-induced formation of radical anion peptides. Electron photodetachment dissociation experiments. Rapid Commun. Mass Spectrom 21, 265-268 (2007)
46. McAlister, G.C., Russell, J.D., Rumachik, N.G., Hebert, A.S., Syka, J.E.P., Geer, L.Y., Westphall, M.S., Pagliarini, D.J., Coon, J.J.: Analysis of the acidic proteome with negative electron-transfer dissociation mass spectrometry. Anal. Chem. 84, 2875-2882 (2012)
47. Madsen, J.A., Xu, H., Horton, A.P., Boutz, D.R., Kaoud, T.S., Dalby, K.N., Brodbelt, J.S.: A flexible searching algorithm for acidic proteome characterization by UVPD of peptide anions, unpublished (submitted)
48. Xu, H., Freitas, M.: A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data. BMC Bioinformatics 8, 133 (2007)
49. Xu, H., Zhang, L., Freitas, M.A.: Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine. J. Proteome Res. 7, 138-144 (2008)
50. Xu, H., Hsu, P.-H., Zhang, L., Tsai, M.-D., Freitas, M.A.: Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry. J. Proteome Res. 9, 3384-3393 (2010)