Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation

Journal of the American Society for Mass Spectrometry

Volumn 26, Issue 5, 2015, Pages 782-787

  Durbin, Kenneth R ^a   Skinner, Owen S ^a   Fellers, Ryan T ^a   Kelleher, Neil L ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Internal fragmentation; Proteomics; Top down mass spectrometry

Indexed keywords

ISOTOPES; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS; SPECTROMETRY;

COLLISIONAL DISSOCIATION; FRAGMENTATION CHANNELS; FRAGMENTATION PROCESS; INTERNAL FRAGMENTATION; PROTEOMICS; SEQUENCE COVERAGES; TOP-DOWN MASS SPECTROMETRIES; VOLTAGE POTENTIALS;

IONS;

UBIQUITIN; PEPTIDE FRAGMENT;

ALGORITHM; ARTICLE; COLLISIONALLY ACTIVATED DISSOCIATION; ELECTRIC POTENTIAL; ELECTROSPRAY MASS SPECTROMETRY; ENERGY; FRAGMENTATION REACTION; PROTEIN ANALYSIS; RADIOISOTOPE DISTRIBUTION; TANDEM MASS SPECTROMETRY; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; BOVINE; CHEMISTRY; COMPARATIVE STUDY; MOLECULAR MODEL; PEPTIDE MAPPING; PROCEDURES; PROTEIN DEGRADATION; PROTEIN DENATURATION; VOLATILIZATION;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; PROTEIN DENATURATION; PROTEOLYSIS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY; UBIQUITIN; VOLATILIZATION;

EID: 84928955720     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-015-1078-1     Document Type: Article

References (15)

1. Durbin, K.R., Fellers, R.T., Ntai, L., Kelleher, N.L., Compton, P.D.: Autopilot: an online data acquisition control system for the enhanced high-throughput characterization of intact proteins. Anal. Chem. 86, 1485-92 (2014)
2. Zamdborg, L., LeDuc, R.D., Glowacz, K.J., Kim, Y.-B., Viswanathan, V., Spaulding, I.T., Early, B.P., Bluhm, E.J., Babai, S., Kelleher, N.L.: ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. Nucleic Acids Res. 35, W701-6 (2007)
3. Shaw, J.B., Li, W., Holden, D.D., Zhang, Y., Griep-Raming, J., Fellers, R.T., Early, B.P., Thomas, P.M., Kelleher, N.L., Brodbelt, J.S.: Complete protein characterization using top-down mass spectrometry and ultraviolet photodissociation. J. Am. Chem. Soc. 135, 12646-51 (2013)
4. Karabacak, N.M., Li, L., Tiwari, A., Hayward, L.J., Hong, P., Easterling, M.L., Agar, J.N.: Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Mol. Cell Proteomics 8, 846-56 (2009)
5. Breuker, K., Jin, M., Han, X., Jiang, H., McLafferty, F.W.: Top-down identification and characterization of biomolecules by mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 1045-53 (2008)
6. Ballard, K.D., Gaskell, S.J.: Sequential mass-spectrometry applied to the study of the formation of internal fragment ions of protonated peptides. Int. J. Mass Spectrom. Ion Process 111, 173-189 (1991)
7. Khatun, J., Ramkissoon, K., Giddings, M.C.: Fragmentation characteristics of collision-induced dissociation in MALDI TOF/TOF mass spectrometry. Anal. Chem. 79, 3032-40 (2007)
8. Barran, P.E., Polfer, N.C., Campopiano, D.J., Clarke, D.J., Langridge-Smith, P.R.R., Langley, R.J., Govan, J.R.W., Maxwell, A., Dorin, J.R., Millar, R.P., Bowers, M.T.: Is it biologically relevant to measure the structures of small peptides in the gas phase? Int. J. Mass Spectrom. 240, 273-84 (2005)
9. Skinner, O.S., McLafferty, F.W., Breuker, K.: How ubiquitin unfolds after transfer into the gas phase. J. Am. Soc. Mass Spectrom. 23, 1011-4 (2012)
10. Cobb, J.S., Easterling, M.L., Agar, J.N.: Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides. J. Am. Soc. Mass Spectrom. 21, 949-59 (2010)
11. Price, W.D., Williams, E.R.: Activation of peptide ions by blackbody radiation: factors that lead to dissociation kinetics in the rapid energy exchange limit. J. Phys. Chem. A 101, 8844-52 (1997)
12. Smith, L.M., Kelleher, N.L., The Consortium for Top Down Proteomics: Proteoform: a single term describing protein complexity. Nat. Methods 10, 186-7 (2013)
13. LeDuc, R.D., Fellers, R.T., Early, B.P., Greer, J.B., Thomas, P.M., Kelleher, N.L.: The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. J. Proteome Res. 13, 3231-40 (2014)
14. Harvey, S.R., Porrini, M., Konijnenberg, A., Clarke, D.J., Tyler, R.C., Langridge-Smith, P.R.R., MacPhee, C.E., Volkman, B.F., Barran, P.E.: Dissecting the dynamic conformations of the metamorphic protein lymphotactin. J. Phys. Chem. B 118, 12348-59 (2014)
15. Kruger, N.A., Zubarev, R.A., Carpenter, B.K., Kelleher, N.L., Horn, D.M., McLafferty, F.W.: Electron capture versus energetic dissociation of protein ions. Int. J. Mass Spectrom. 182, 1-5 (1999)