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J Biomol Tech. 2010 September; 21(3 Suppl): S38.
PMCID: PMC2918003

Electron Transfer Dissociation on Small Intact Proteins in an Ultra High Resolution Quadrupole Time of Flight Mass Spectrometer

C. Stoermer,1 D.A. Kaplan,2 R. Hartmer,1 M. Lubeck,1 O. Raether,1 and M.A. Park2
1Bruker Daltonics Inc., Billerica, MA, United States;
2Bruker Daltonik GmbH, Bremen, Germany;
3Bruker Daltonics Inc., Fremont, CA, United States



Electron Transfer Dissociation (ETD) has become a powerful technique for characterizing post translational modifications of proteins. Requiring interaction of both, analyte as well as ETD reagent ions, ETD is most commonly implemented in trapping instruments like 2D or 3D ion traps, providing low acquisition speed and mass accuracy. In contrast, Orthogonal Time of Flight (OTOF) instruments feature very high acquisition speed, mass accuracy, and in-spectra dynamic range. We present an instrument merging the trapping technique of ETD with an ultra high resolution quadrupole TOF, providing a resolution of 40,000, a mass accuracy <2ppm and an LC compatible spectra rate. The instrument used for this work is a Bruker ETD-maXis quadrupole TOF. ETD reagent anions were generated in an nCI source and are orthogonally injected between a pair of octapoles; which along with the nCI source were adapted from amaZon ETD ion trap. Reagent and analyte ions were mass selectively transmitted through a mass resolving quad and trapped in a hexapole collision cell. After the ETD reaction, product ions are transferred to a cooling cell where they are stored and extracted to the TOF analyzer. While ions are extracted, the next ETD experiment is ongoing in the collision cell thus maximizing duty cycle. ETD MS/MS data of intact proteins show a very complex mixture of ETD product ions, where the high resolution and mass accuracy capability of the TOF instrument was more than sufficient for protein identification with Mascot data base search of the intact protein. The work thus far shows a novel ultra-high resolution quadrupole TOF that is capable of rapid ETD experiments with sufficient resolving power for ETD MS/MS analysis of small intact proteins. We will present ETD MS/MS of proteins samples (ubiquitin, cytochrome C, beta-casein and carbonic anhydrase) resulting in sequence coverage of up to 90%.

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