Mobile and localized protons: a framework for understanding peptide dissociation

Area of Science:

• Analytical Chemistry
• Biochemistry
• Proteomics

Background:

• Tandem mass spectrometry (MS/MS) is crucial for protein identification and peptide sequencing.
• Peptide fragmentation patterns, specifically b and y ions from amide bond cleavage, are fundamental to MS/MS.
• Understanding non-canonical fragmentation, or enhanced cleavage, is key to improving sequencing accuracy.

Purpose of the Study:

• To refine the mobile proton model for peptide fragmentation in MS/MS.
• To elucidate the mechanisms behind enhanced cleavage at aspartic acid (Asp) and histidine (His) residues.
• To improve the accuracy of protein identification and peptide sequencing using mass spectrometry.

Main Methods:

• Utilized surface-induced dissociation (SID) and gas-phase collision-induced dissociation (CID).
• Investigated peptide fragmentation under various experimental conditions.
• Applied the refined mobile proton model to analyze fragmentation pathways.

Main Results:

• Demonstrated enhanced cleavage at Asp residues via side-chain acidic proton initiating C-terminal amide bond cleavage, forming anhydrides.
• Showed enhanced cleavage at protonated His residues involves side-chain proton transfer and nucleophilic attack, forming cyclic structures.
• Differentiated mechanisms of enhanced cleavage at acidic (Asp) versus basic (His) residues.

Conclusions:

• The mobile proton model successfully explains enhanced peptide fragmentation at Asp and His residues.
• Specific mechanisms involving side-chain protonation and nucleophilic attack drive enhanced cleavage at these residues.
• Accurate interpretation of these fragmentation patterns enhances the reliability of peptide sequencing and protein identification in proteomics.