Protein Characterization Improved with ETD Ion Source

Dr. Karger and Research Associate Professor Billy Wu have developed new methods which capitalize on electron transfer dissociation (ETD) ionization to greatly improve detection of post-translational modications. 

Traditionally, peptides are fragmented using collision-induced dissociation (CID), which breaks the weakest bonds and produces a characteristic series of fragments. Many important posttranslational modifications, however, are fragile and are lost in the CID collision process. Electron-transfer dissociation (ETD) cleaves selectively on the peptide backbone, leaving post-translational modifications intact. Additionally, ETD produces a different set of fragments that are complementary to CID, so sequence coverage is more complete. 

The Institute recently acquired a Thermo-Fisher LTQ-XL instrument with an ETD source on the back end of the linear ion trap. (The electrospray source is on the front-end of the system.)  The linear ion trap can be used to pre-select ions or fragments of interest for ETD fragmentation. The new LTQ-XL mass spectrometer with ETD is a powerful complement to our LTQ-FT hybrid mass spectrometer, which combines a linear ion-trap mass spectrometer with a Fourier Transform mass spectrometer (FT-MS). In the LTQFT, the linear ion-trap can be used to pre-select ions or fragments of interest for high-resolution FT-MS analysis of intact proteins or larger peptide fragments. 

A paper showing the improvements in analysis of glycosylation and phosphorylation has been published (1), and another paper on the use of ETD to map disulphide bonding has been submitted for publication. Work is in progress to show deamidation can be quantitated and correlated with other modifications.

(1) Wu SL, Hühmer AF, Hao Z, Karger BL. "On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications."  J Proteome Res. 6(11):4230-44. (2007) pubmed