Characterization of electron transfer dissociation in the orbitrap velos HCD cell

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 11, 2013, Pages 1663-1670

  Frese, Christian K ^a,b   Nolting, Dirk ^c   Altelaar, A F Maarten ^a,b   Griep Raming, Jens ^c   Mohammed, Shabaz ^a,b,d   Heck, Albert J R ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

^c THERMO FISHER SCIENTIFIC   (Germany)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Electron transfer dissociation; Protein sequencing; Top down proteomics

Indexed keywords

COLLISION CELLS; ELECTRON TRANSFER DISSOCIATION; ELECTRON-TRANSFER REACTIONS; MODE OF OPERATIONS; PROTEIN SEQUENCING; PROTEOMICS; SEQUENCE ANALYSIS; TRYPTIC PEPTIDES;

CELLS; CYTOLOGY; DISSOCIATION; IONS; MOLECULAR BIOLOGY; PROTEINS;

ELECTRON TRANSITIONS;

ANION; CATION; TRYPSIN; UBIQUITIN;

ARTICLE; CELL TYPE; DIRECT CURRENT; ELECTRIC POTENTIAL; ELECTRON TRANSFER DISSOCIATION; ELECTRON TRANSPORT; HCD CELL; HUMAN; HUMAN CELL; ION TRAP ELECTRON TRANSFER DISSOCIATION; ION TRAP MASS SPECTROMETRY; PROTEOMICS; SEQUENCE ANALYSIS;

CATIONS; ELECTRONS; HELA CELLS; HUMANS; IONS; MASS SPECTROMETRY; PEPTIDE FRAGMENTS; PEPTIDES; TANDEM MASS SPECTROMETRY; UBIQUITIN;

EID: 84885643559     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-013-0618-9     Document Type: Article

References (51)

1. 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)
2. McLafferty, F.W.; Horn, D.M.; Breuker, K.; Ge, Y.; Lewis, M.A.; Cerda, B.; Zubarev, R.A.; Carpenter, B.K.: Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J Am Soc Mass Spectrom 12, 245-249 (2001)
3. Silivra, O.A.; Kjeldsen, F.; Ivonin, I.A.; Zubarev, R.A.: Electron capture dissociation of polypeptides in a three-dimensional quadrupole ion trap: Implementation and first results. J Am Soc Mass Spectrom 16, 22-27 (2005)
4. Baba, T.; Hashimoto, Y.; Hasegawa, H.; Hirabayashi, A.; Waki, I.: Electron capture dissociation in a radio frequency ion trap. Anal Chem 76, 4263-4266 (2004)
5. Satake, H.; Hasegawa, H.; Hirabayashi, A.; Hashimoto, Y.; Baba, T.; Masuda, K.: Fast multiple electron capture dissociation in a linear radio frequency quadrupole ion trap. Anal Chem 79, 8755-8761 (2007)
6. Kjeldsen, F.; Haselmann, K.F.; Budnik, B.A.; Jensen, F.; Zubarev, R.A.: Dissociative capture of hot (3-13 eV) electrons by polypeptide polycations: An efficient process accompanied by secondary fragmentation. Chem Phys Lett 356, 201-206 (2002)
7. Axelsson, J.; Palmblad, M.; Hakansson, K.; Hakansson, P.: Electron capture dissociation of substance P using a commercially available Fourier transform ion cyclotron resonance mass spectrometer. Rapid Commun Mass Spectrom 13, 474-477 (1999)
8. Voinov, V.G.; Deinzer, M.L.; Beckman, J.S.; Barofsky, D.F.: Electron capture collision-induced, and electron capture-collision induced dissociation in Q-TOF. J Am Soc Mass Spectrom 22, 607-611 (2011)
9. Ding, L.; Brancia, F.L.: Electron capture dissociation in a digital ion trap mass spectrometer. Anal Chem 78, 1995-2000 (2006)
10. Syka, J.E.; 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 101, 9528-9533 (2004)
11. Chi, A.; Huttenhower, C.; Geer, L.Y.; Coon, J.J.; Syka, J.E.; Bai, D.L.; Shabanowitz, J.; Burke, D.J.; Troyanskaya, O.G.; Hunt, D.F.: Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A 104, 2193-2198 (2007)
12. 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 259, 197-203 (2007)
13. Kim, M.S.; Pandey, A.: Electron transfer dissociation mass spectrometry in proteomics. Proteomics 12, 530-542 (2012)
14. Mikesh, L.M.; Ueberheide, B.; Chi, A.; Coon, J.J.; Syka, J.E.; Shabanowitz, J.; Hunt, D.F.: The utility of ETD mass spectrometry in proteomic analysis. Biochim Biophys Acta 1764, 1811-1822 (2006)
15. Coon, J.J.; Ueberheide, B.; Syka, J.E.P.; Dryhurst, D.D.; Ausio, J.; Shabanowitz, J.; Hunt, D.F.: Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc Natl Acad Sci U S A 102, 9463-9468 (2005)
16. Frese, C.K.; Altelaar, A.F.; Hennrich, M.L.; Nolting, D.; Zeller, M.; Griep-Raming, J.; Heck, A.J.; Mohammed, S.: Improved peptide identification by targeted fragmentation using CID, HCD, and ETD on an LTQ-Orbitrap Velos. J Proteome Res 10, 2377-2388 (2011)
17. Zubarev, R.A.; Zubarev, A.R.; Savitski, M.M.: Electron capture/transfer versus collisionally activated/induced dissociations: Solo or duet? J Am Soc Mass Spectrom 19, 753-761 (2008)
18. Coon, J.J.: Collisions or electrons? Protein sequence analysis in the 21st century. Anal Chem 81, 3208-3215 (2009)
19. Zhang, Q.B.; Frolov, A.; Tang, N.; Hoffmann, R.; van de Goor, T.; Metz, T.O.; Smith, R.D.: Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides. Rapid Commun Mass Spectrom 21, 661-666 (2007)
20. Molina, H.; Horn, D.M.; Tang, N.; Mathivanan, S.; Pandey, A.: Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A 104, 2199-2204 (2007)
21. Bunger, M.K.; Cargile, B.J.; Ngunjiri, A.; Bundy, J.L.; Stephenson, J.L.: Automated proteomics of E coli via top-down electron-transfer dissociation mass spectrometry. Anal Chem 80, 1459-1467 (2008)
22. Siuti, N.; Kelleher, N.L.: Decoding protein modifications using top-down mass spectrometry. Nature Methods 4, 817-821 (2007)
23. Fornelli, L.; Damoc, E.; Thomas, P.M.; Kelleher, N.L.; Aizikov, K.; Denisov, E.; Makarov, A.; Tsybin, Y.O. Analysis of intact monoclonal antibody IgG1 by electron transfer dissociation Orbitrap FTMS. Mol Cell Proteomics 11, 1758-1767 (2012)
24. Xia, Y.; Chrisman, P.A.; Erickson, D.E.; Liu, J.; Liang, X.; Londry, F.A.; Yang, M.J.; McLuckey, S.A.: Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer. Anal Chem 78, 4146-4154 (2006)
25. Pitteri, S.J.; Chrisman, P.A.; Hogan, J.M.; McLuckey, S.A.: Electron transfer ion/ion reactions in a three-dimensional quadrupole ion trap: Reactions of doubly and triply protonated peptides with SO2*. Anal Chem 77, 1831-1839 (2005)
26. McAlister, G.C.; Berggren, W.T.; Griep-Raming, J.; Horning, S.; Makarov, A.; Phanstiel, D.; Stafford, G.; Swaney, D.L.; Syka, J.E.; Zabrouskov, V.; Coon, J.J.: A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res 7, 3127-3136 (2008)
27. Kaplan, D.A.; Hartmer, R.; Speir, J.P.; Stoermer, C.; Gumerov, D.; Easterling, M.L.; Brekenfeld, A.; Kim, T.; Laukien, F.; Park, M.A.: Electron transfer dissociation in the hexapole collision cell of a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer. Rapid Commun Mass Spectrom 22, 271-278 (2008)
28. Hunt, D.F.; Yates III, J.R.; Shabanowitz, J.; Winston, S.; Hauer, C.R.: Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci USA 83, 6233-6237 (1986)
29. McAlister, G.C.; Phanstiel, D.; Good, D.M.; Berggren, W.T.; Coon, J.J.: Implementation of electron-transfer dissociation on a hybrid linear ion trap-Orbitrap mass spectrometer. Anal Chem 79, 3525-3534 (2007)
30. Huang, T.Y.; Emory, J.F.; O'Hair, R.A.J.; McLuckey, S.A.: Electron-transfer reagent anion formation via electrospray ionization and collision-induced dissociation. Anal Chem 78, 7387-7391 (2006)
31. Wu, J.; Hager, J.W.; Xia, Y.; Londry, F.A.; McLuckey, S.A.: Positive ion transmission mode ion/ion reactions in a hybrid linear ion trap. Anal Chem 76, 5006-5015 (2004)
32. Liang, X.; Hager, J.W.; McLuckey, S.A.: Transmission mode ion/ion electron-transfer dissociation in a linear ion trap. Anal Chem 79, 3363-3370 (2007)
33. Xia, Y.; Wu, J.; McLuckey, S.A.; Londry, F.A.; Hager, J.W.: Mutual storage mode ion/ion reactions in a hybrid linear ion trap. J Am Soc Mass Spectrom 16, 71-81 (2005)
34. 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)
35. Russell, J.D.; Ledvina, A.R.; McAlister, G.C.; Westphall, M.S.; Syka, J.E.; Griep-Raming, J.; Coon, J.J. Single-scan, top-down intact protein analysis on a Velos Orbitrap modified with a dedicated high-capacity ion/ion reaction cell. Proceedings of the 59th ASMS Conference on Mass Spectrometry and Allied Topics; Denver, CO, (2011)
36. Yang, C.; Russell, J.D.; Ledvina, A.R.; Westphall, M.S.; Brumbaugh, J.; Coon, J.J. Profiling histone H3 isoforms in human embryonic stem cells using a Velos Orbitrap modified with a segmented reaction cell. Proceedings of the 59th ASMS Conference on Mass Spectrometry and Allied Topics; Denver, CO, (2011)
37. Frese, C.K.; Altelaar, M.; van den Toorn, H.W.; Nolting, D.; Griep-Raming, J.; Heck, A.J.; Mohammed, S. Towards full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Anal Chem 84, 9668-9673 (2012)
38. Nolting, D.; Griep-Raming, J.; Malek, R.; Makarov, A. Implementation of ETD reactions in a linear quadrupole collision cell utilizing a static DC gradient for dual ion trapping. Proceedings of the 58th ASMS Conference on Mass Spectrometry and Allied Topics; Salt Lake City, UT, (2010)
39. Chalkley, R.J.; Medzihradszky, K.F.; Lynn, A.J.; Baker, P.R.; Burlingame, A.L.: Statistical analysis of peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem 82, 579-584 (2010)
40. Mansoori, B.A.; Dyer, E.W.; Lock, C.M.; Bateman, K.; Boyd, R.K.; Thomson, B.A.: Analytical performance of a high-pressure radio frequency-only quadrupole collision cell with an axial field applied by using conical rods. J Am Soc Mass Spectrom 9, 775-788 (1998)
41. Loboda, A.; Krutchinsky, A.; Loboda, O.; McNabb, J.; Spicer, V.; Ens, W.; Standing, K.: Novel Linac II electrode geometry for creating an axial field in a multipole ion guide. Eur J Mass Spectrom 6, 531-536 (2000)
42. Hakansson, K.; Chalmers, M.J.; Quinn, J.P.; McFarland, M.A.; Hendrickson, C.L.; Marshall, A.G.: Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. Anal Chem 75, 3256-3262 (2003)
43. Sze, S.K.; Ge, Y.; Oh, H.; McLafferty, F.W.: Plasma electron capture dissociation for the characterization of large proteins by top down mass spectrometry. Anal Chem 75, 1599-1603 (2003)
44. 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)
45. Breuker, K.; Oh, H.B.; Horn, D.M.; Cerda, B.A.; McLafferty, F.W.: Detailed unfolding and folding of gaseous ubiquitin ions characterized by electron capture dissociation. J Am Chem Soc 124, 6407-6642 (2002)
46. McLafferty, F.W.; Fridriksson, E.K.; Horn, D.M.; Lewis, M.A.; Zubarev, R.A.: Biochemistry-biomolecule mass spectrometry. Science 284, 1289-1290 (1999)
47. Horn, D.M.; Zubarev, R.A.; McLafferty, F.W.: Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry. Proc Natl Acad Sci U S A 97, 10313-10317 (2000)
48. Robinson, E.W.; Leib, R.D.; Williams, E.R.: The role of conformation on electron capture dissociation of ubiquitin. J Am Soc Mass Spectrom 17, 1469-1479 (2006)
49. Mikhailov, V.A.; Cooper, H.J.: Activated ion electron capture dissociation (AI ECD) of proteins: synchronization of infrared and electron irradiation with ion magnetron motion. J Am Soc Mass Spectrom 20, 763-771 (2009)
50. Schnier, P.D.; Gross, D.S.; Williams, E.R.: On the maximum charge-state and proton-transfer reactivity of peptide and protein ions formed by electrospray-ionization. J Am Soc Mass Spectrom 6, 1086-1097 (1995)
51. Li, W.; Song, C.; Bailey, D.J.; Tseng, G.C.; Coon, J.J.; Wysocki, V.H.: Statistical analysis of electron transfer dissociation pairwise fragmentation patterns. Anal Chem 83, 9540-9545 (2011)