Electron Transfer Dissociation (ETD)

Electron transfer dissociation is an innovative ion fragmentation technology that makes it possible to identify and determine the locations of labile post-translational modifications (PTMs) on peptides or intact proteins. ETD can also produce excellent sequence information for very basic proteins such as histones that do not fragment well by standard collision induced dissociation (CID). Adding ETD capability to an LTQ ion trap or LTQ Orbitrap hybrid mass spectrometer makes it possible to characterize complex PTMs, revealing aspects of the proteome that were previously inaccessible. It enables investigation of biologically important functional groups on peptides involved in crucial regulatory events in cells.

Providing sequence information and modification locations that CID can’t

Collision-induced dissociation, the fragmentation technique most commonly used in multi-stage mass spectrometry, produces primarily b- and y-type peptide fragment ions. Spectra generated by CID are often sufficient for determining peptide sequences. However, in proteins that have undergone a post-translational modification (PTM) such as glycosylation, phosphorylation, sulfonation, or nitrosylation, or a chemical modification such as PEG-ylation, CID preferentially cleaves the weakly bound modification off the peptide backbone and leaves the backbone mostly intact. The resulting spectra provide little information about the structure of the peptide or the location of the modification.

ETD uses reagent gas anions and gas-phase ion/ion chemistry to induce fragmentation along the peptide backbone in a sequence-independent manner. It produces primarily c- and z-type fragment ions and leaves modifications linked to the peptide chain. This allows straightforward identification of the peptide sequence and the site of modification.

Available on ion trap and Orbitrap mass spectrometers

ETD is available on Thermo Scientific LTQ XL and Velos linear ion trap and LTQ Orbitrap XL and Velos hybrid mass spectrometers. Both instrument types can acquire highly complementary CID and ETD data in a single run. When the data are combined, the result is often significantly greater sequence coverage than is afforded by either technique alone. This greater sequence coverage can improve results of top-down, middle down, or bottom-up protein identification as well as protein structural analysis.

Software to get the most from every analysis

Many popular search algorithms are not optimized for ETD data and are not designed to interrogate c- and z-type ions. Thermo Scientific Proteome Discoverer software includes a new ETD database search algorithm called Z-Core that was designed specifically to accommodate the unique characteristics of ETD spectra. Proteome Discoverer software facilitates the merging of ETD and CID search results, increasing sequence coverage and the certainty of peptide and protein identifications.