Abstract
We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section rf ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion–ion reactions. The approximately 2-fold higher quadrupole field frequency of this cell relative to that of the A-QLT enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell’s longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation.
Similar content being viewed by others
References
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. 101(26), 9528–9533 (2004)
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(1/3), 33–42 (2004)
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(13), 3265–3266 (1998)
Kelleher, N.L.: Top-down proteomics. Anal. Chem. 76(11), 196A–203A (2004)
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(1/3), 197–203 (2007)
Tsybin, Y.O., Fornelli, L., Stoermer, C., Luebeck, M., Parra, J., Nallet, S., Wurm, F.M., Hartmer, R.: Structural analysis of intact monoclonal antibodies by electron transfer dissociation mass spectrometry. (Translated from English). Anal. Chem. 83(23), 8919–8927 (2011) (in English)
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. (Translated from English). Mol. Cell. Proteomics 11(12), 1758–1767 (2012) (in English)
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(17), 5006–5015 (2004)
Liang, X., Hager, J.W., McLuckey, S.A.: Transmission mode ion/ion electron-transfer dissociation in a linear ion trap. Anal. Chem. 79(9), 3363–3370 (2007)
Rand, K., Pringle, S., Morris, M., Engen, J., Brown, J.: ETD in a traveling wave ion guide at tuned z-spray ion source conditions allows for site-specific hydrogen/deuterium exchange measurements. J. Am. Soc. Mass Spectrom. 22(10), 1784–1793 (2011)
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(12), 4146–4154 (2006)
Xia, Y., Thomson, B.A., McLuckey, S.A.: Bidirectional ion transfer between quadrupole arrays: MSn ion/ion reaction experiments on a quadrupole/time-of-flight tandem mass spectrometer. Anal. Chem. 79(21), 8199–8206 (2007)
Huang T-y McLuckey, S.A.: Top-down protein characterization facilitated by ion/ion reactions on a quadrupole/time of flight platform. Proteomics 10(20), 3577–3588 (2010)
McAlister, G.C., Berggren, W.T., Griep-Raming, J., Horning, S., Makarov, A., Phanstiel, D., Stafford, G., Swaney, D.L., Syka, J.E.P., Zabrouskov, V., Coon, J.J.: A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer. J Proteome Res 7(8), 3127–3136 (2008)
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(10), 3525–3534 (2007)
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(3), 271–278 (2008)
Hartmer, R., Lubeck, M.: New approach for characterization of post translational modified peptides using ion trap MS with combined ETD/CID fragmentation. LC-GC Eur. 18, 11–13 (2005)
Sobott, F., Watt, S.J., Smith, J., Edelmann, M.J., Kramer, H.B., Kessler, B.M.: Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination. (Translated from English). J. Am. Soc. Mass Spectrom. 20(9), 1652–1659 (2009) (in English)
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(6), 1831–1839 (2005)
Olsen, J.V., Schwartz, J.C., Griep-Raming, J., Nielsen, M.L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., Wouters, E.R., Senko, M., Makarov, A., Mann, M., Horning, S.: A dual pressure linear ion trap orbitrap instrument with very high sequencing speed. Mol. Cell. Proteomics 8(12), 2759–2769 (2009)
Russell, J.D., Ledvina, A.R., McAlister, G.C., Westphall, M.S., Syka, J.E.P., Griep-Raming, J., Coon, J.J.: Single scan, top-down intact protien analysis of 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, June, Denver, CO (2011)
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, June, Denver, CO (2011)
Ledvina, A.R., Beauchene, N.A., McAlister, G.C., Syka, J.E.P., Schwartz, J.C., Griep-Raming, J., Westphall, M.S., Coon, J.J.: Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture. (Translated from English). Anal. Chem. 82(24), 10068–10074 (2010) (in English)
Ledvina, A.R., McAlister, G.C., Gardner, M.W., Smith, S.I., Madsen, J.A., Schwartz, J.C., Stafford, G.C., Syka, J.E.P., Brodbelt, J.S., Coon, J.J.: Infrared photoactivation reduces peptide folding and hydrogen-atom migration following ETD tandem mass spectrometry. (Translated from English). Angew. Chem.-Int. Edit. 48(45), 8526–8528 (2009) (in English)
Schaub, T.M., Hendrickson, C.L., Horning, S., Quinn, J.P., Senko, M.W., Marshall, A.G.: High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 tesla. (Translated from English). Anal. Chem. 80(11), 3985–3990 (2008) (in English)
Tsybin, Y.O., Witt, M., Baykut, G., Hakansson, P.: Electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry in the electron energy range 0–50 eV. Rapid Commun. Mass Spectrom. 18(14), 1607–1613 (2004)
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. (Translated from English). Anal. Chem. 75(13), 3256–3262 (2003) (in English)
Swaney, D.L., McAlister, G.C., Coon, J.J.: Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5(11), 959–964 (2008)
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(6), 2875–2882 (2012)
Ficarro, S.B., Zhang, Y., Lu, Y., Moghimi, A.R., Askenazi, M., Hyatt, E., Smith, E.D., Boyer, L., Schlaeger, T.M., Luckey, C.J., Marto, J.A.: Improved electrospray ionization efficiency compensates for diminished chromatographic resolution and enables proteomics analysis of tyrosine signaling in embryonic stem cells. Anal. Chem. 81(9), 3440–3447 (2009)
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(suppl_2), W701–W706 (2007)
LeDuc, R.D., Kelleher, N.L.: Using ProSight PTM and related tools for targeted protein identification and characterization with high mass accuracy tandem MS data. Curr. Protoc. Bioinform. 13(16), 11–28 (2007)
McAlister, G.C., Phanstiel, D.H., Brumbaugh, J., Westphall, M.S., Coon, J.J.: Higher-energy collision-activated dissociation without a dedicated collision cell. Mol. Cell. Proteom. 10(5):1–6 (2011)
Compton, P.D., Strukl, J.V., Bai, D.L., Shabanowitz, J., Hunt, D.F.: Optimization of electron transfer dissociation via informed selection of reagents and operating parameters. Anal. Chem. 84(3), 1781–1785 (2012)
McLuckey, S.A., Stephenson, J.L., Asano, K.G.: Ion/ion proton-transfer kinetics: Implications for analysis of ions derived from electrospray of protein mixtures. Anal. Chem. 70(6), 1198–1202 (1998)
Tolmachev, A.V., Udseth, H.R., Smith, R.D.: Modeling the ion density distribution in collisional cooling RF multipole ion guides. Int. J. Mass Spectrom. 222(1), 155–174 (2003)
McAlister, G.C., Phanstiel, D.P., Coon, J.J.: A dual reaction cell, ETD-enabled orbitrap mass spectrometer for top-down proteomics. 56th Proceedings of the American Society for Mass Spectrometry and Allied Topics Conference, June, Denver, CO, USA (2008)
Schwartz, J., Senko, M., Syka, J.: A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 13(6), 659–669 (2002)
Michalski, A., Damoc, E., Lange, O., Denisov, E., Nolting, D., Müller, M., Viner, R., Schwartz, J., Remes, P., Belford, M., Dunyach, J.-J., Cox, J., Horning, S., Mann, M., Makarov, A.: Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 11(3), 1–11 (2012)
Makarov, A., Denisov, E., Kholomeev, A., Balschun, W., Lange, O., Strupat, K., Horning, S.: Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78(7), 2113–2120 (2006)
Perry, R.H., Cooks, R.G., Noll, R.J.: Orbitrap mass spectrometry: Instrumentation, ion motion and applications. Mass Spectrom. Rev. 27(6), 661–699 (2008)
Alexander M.: Theory and practice of the Orbitrap mass analyzer. In: Practical Aspects of Trapped Ion Mass Spectrometry, Vol. IV, pp. 251–272. CRC Press, Boca Raton, FL, USA (2010)
Cech, N.B., Enke, C.G.: Practical implications of some recent studies in electrospray ionization fundamentals. Mass Spectrom. Rev. 20(6), 362–387 (2001)
Taylor, G.K., Kim, Y.-B., Forbes, A.J., Meng, F., McCarthy, R., Kelleher, N.L.: Web and database software for identification of intact proteins using “top down” mass spectrometry. Anal. Chem. 75(16), 4081–4086 (2003)
LeDuc, R.D., Taylor, G.K., Kim, Y.-B., Januszyk, T.E., Bynum, L.H., Sola, J.V., Garavelli, J.S., Kelleher, N.L.: ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res. 32(suppl_2), W340–W345 (2004)
Yergey, J.A.: A general approach to calculating isotopic distributions for mass spectrometry. Int. J. Mass Spec. Ion Phys. 52(2/3), 337–349 (1983)
Rockwood, A.L., Van Orden, S.L., Smith, R.D.: Rapid calculation of isotope distributions. Anal. Chem. 67(15), 2699–2704 (1995)
Senko, M.W., Beu, S.C., McLafferty, F.W.: Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6(4), 229–233 (1995)
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. 11(4), 320–332 (2000)
Renard, B., Kirchner, M., Steen, H., Steen, J., Hamprecht, F.: NITPICK: peak identification for mass spectrometry data. BMC Bioinforma. 9(1), 355 (2008)
Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J., Anderson, G., Smith, R.: Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinforma. 10, 87 (2009)
Tran, J.C., Zamdborg, L., Ahlf, D.R., Lee, J.E., Catherman, A.D., Durbin, K.R., Tipton, J.D., Vellaichamy, A., Kellie, J.F., Li, M., Wu, C., Sweet, S.M.M., Early, B.P., Siuti, N., LeDuc, R.D., Compton, P.D., Thomas, P.M., Kelleher, N.L.: Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480(7376), 254–258 (2011)
Acknowledgments
The authors gratefully acknowledge support from Thermo Fisher Scientific, NSF CAREER grant 0747990, and NIH grant R01 GM080148. C.M.R was funded by an NSF Graduate Research Fellowship and NIH Traineeship (T32GM008505).
Author information
Authors and Affiliations
Corresponding author
Additional information
Christopher M. Rose and Jason D. Russell contributed equally to this work.
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
ESM 1
(DOCX 494 kb)
Rights and permissions
About this article
Cite this article
Rose, C.M., Russell, J.D., Ledvina, A.R. et al. Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species. J. Am. Soc. Mass Spectrom. 24, 816–827 (2013). https://doi.org/10.1007/s13361-013-0622-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13361-013-0622-0