Abstract
In the present study, we report that the charge-directed (assisted) peptide dissociation products, such as b- and y-type peptidebackbone fragments, were the major products in MS/MS and MS3 applications of some o-TEMPO-Bz-C(O)-peptide ions, whileradical-driven dissociation products, such as a/x and c/z-type fragments, were previously shown to be the major products in the freeradical initiated peptide sequencing mass spectrometry (FRIPS MS). Those o-TEMPO-Bz-C(O)-peptides share a common feature intheir sequences, that is, the peptides do not include an arginine residue that has the highest proton affinity among free amino acids. The appearance of b- and y-type fragments as major products in FRIPS MS can be understood in terms of the so-called “mobile-protonmodel”. When the proton is highly mobilized by the absence of arginine, the chare-directed peptide dissociation pathways appearto be more competitive than the radical-driven dissociation pathways, in our FRIPS experiments.
Highlights
Since the discovery of electron capture dissociation (ECD) in 1998, radical-based peptide/protein tandem mass spectrometry has been the area of active research due to its powerful peptide dissociation capability and its unique opportunity for characterization of post-translational modifications.[1,2,3,4,5,6,7,8,9,10,11,12,13,14]
It was shown that a radical site could be generated on the peptide backbone through electron transfer from the negativelycharged anion to the protonated peptide cation; electron transfer dissociation (ETD).[15]
A hint why these conjugated peptides show abnormal Free Radical Initiated Peptide Sequencing (FRIPS) dissociation behaviour may be found in the fact that these three peptides do not include an arginine (R) residue, which is known to have the highest proton affinity among twenty free amino acids,[28] in their sequences
Summary
Since the discovery of electron capture dissociation (ECD) in 1998, radical-based peptide/protein tandem mass spectrometry has been the area of active research due to its powerful peptide dissociation capability and its unique opportunity for characterization of post-translational modifications.[1,2,3,4,5,6,7,8,9,10,11,12,13,14] In ECD, generation of a radical site on the peptide/protein backbone has been shown to be the key step in the ensuing peptide/protein dissociation.[1,3,5] Later, it was shown that a radical site could be generated on the peptide backbone through electron transfer from the negativelycharged anion to the protonated peptide cation; electron transfer dissociation (ETD).[15]These findings have led to the development of a variety of radical-based peptide/protein tandem mass spectrometry methods. The generated radical site was found to result in unique peptide/protein backbone fragmentations upon another collisional activation application.
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