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Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

  • Focus: Electron Transfer Dissociation: Research Article
  • Published:
Journal of The American Society for Mass Spectrometry

Abstract

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO2 laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety’s high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.

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Acknowledgments

The authors gratefully acknowledge support from Thermo Fisher Scientific and NIH grant R01 GM080148. C.M.R was funded by an NSF Graduate Research Fellowship and NIH Traineeship (T32GM008505).

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Authors and Affiliations

  1. Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Aaron R. Ledvina, Christopher M. Rose, Graeme C. McAlister & Joshua J. Coon

  2. Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Joshua J. Coon

  3. Genome Center, University of Wisconsin-Madison, Madison, WI, 53706, USA

    Aaron R. Ledvina, Christopher M. Rose, Michael S. Westphall & Joshua J. Coon

  4. Thermo Fisher Scientific, San Jose, CA, USA

    Jae C. Schwartz

  5. Thermo Fisher Scientific, Bremen, Germany

    Jens Griep-Raming

  6. Thermo Fisher Scientific, Charlottesville, VA, USA

    John E. P. Syka

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  1. Aaron R. Ledvina
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Correspondence to Joshua J. Coon.

Additional information

Aaron R. Ledvina and Christopher M. Rose contributed equally to this work.

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Ledvina, A.R., Rose, C.M., McAlister, G.C. et al. Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer. J. Am. Soc. Mass Spectrom. 24, 1623–1633 (2013). https://doi.org/10.1007/s13361-013-0621-1

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