Collision-induced dissociation (CID), 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. 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, producing primarily c- and z-type fragment ions and leaving modifications linked to the peptide chain. This allows straightforward identification of the peptide sequence and the site of modification.
ETD is available on Thermo Scientific LTQ ion trap and LTQ Orbitrap hybrid mass spectrometers. Both instrument types can acquire complementary CID and ETD data in a single run. When combined, this data can provide significantly greater sequence coverage than either technique by itself. This greater sequence coverage can improve results of top-down, middle down, or bottom-up protein identification as well as protein structural 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 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. 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.
Learn more about ETD options and technique in the following papers and presentations:
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