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J Biomol Tech. 2010 September; 21(3 Suppl): S36.
PMCID: PMC2918156

The Implementation and Characterization of Electron Transfer Dissociation (ETD) on an Ion Mobility Enabled Q-TOF Mass Spectrometer

I. Campuzano,1 J. Brown,1 J. Williams,2 and J. Langridge1
1Waters Corporation, Simonsway, United Kingdom;
2University of Warwick, Warwick, United Kingdom



Electron Transfer Dissociation (ETD) occurs when precursor cations are reacted with radical reagent anions to induce fragmentation. Electron transfer from anion to cation, promotes fast and randomised dissociation and hence ETD product ion spectra contain predominantly “c” and “z” type ions and post translational modifications often remain intact providing valuable sequence information. ETD can be implemented and performed on a hybrid Q-IMS-TOF (Waters Synapt) where a supply of reagent is delivered to the nano ESI source where a high voltage discharge pin generates the reagent anions. Analyte cations were generated by infusion or from a nanoACQUITY UPLC system. For ETD, the ion source polarity and the quadrupole set mass were sequentially switched to deliver anions and cations into the TRAP travelling wave (TWAVE) ion guide where they react to form ETD product ions. Product ions were optionally separated by ion mobility in the IMS TWAVE ion guide or were accelerated into the TRANSFER TWAVE ion guide to cause 2nd generation CID ions prior to mass analysis in the TOF. Tryptic peptides from biological sources were separated by nanoAcquity UPLC and triply charged precursor masses were selected and fragmented to generate LC-ETD spectra. High quality data was observed for single protein tryptic digests at the 20-50fm injection level, with ETD data acquired at 1 spectra/second. Cleavage was observed at almost every amide bond in the peptide backbone, yielding easy-to-interpret sequence ladders of c and z-ions. This coupled with the inherent mass measurement accuracy and resolution of the oa-TOF mass analyser makes the data amenable to de novo sequencing. In addition to the ETD experiments the mass spectrometer can acquire alternate scans in CID, and as such data will be compared and contrasted between ETD and CID on a variety of peptides produced and separated by nanoscale chromatography.

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