A comprehensive investigation of proline fragmentation behavior in low-energy collision-induced dissociation peptide mass spectra

Gas-Phase Fragmentation of Oligoproline Peptide Ions Lacking Easily Mobilizable Protons

“…This would confirm an earlier observation of Dong at al. [38] that the cleavage at N-terminal side of Pro is unfavorable when protons are non-mobile.…”

Energetic switch of the proline effect in collision‐induced dissociation of singly and doubly protonated peptide Ala‐Ala‐Arg‐Pro‐Ala‐Ala

“…Proline effect, the enhancement of cleavage at its N‐terminal amide bond, was commonly observed in fragmentation of protonated peptides in tandem mass spectra under collision‐induced dissociation (CID) condition . However, the selective cleavage was significantly suppressed when Arg or Lys residue located adjacent to the N‐terminal of proline . Interference between adjacent Arg and Pro was also found in the peptide cleavage by trypsin, a most frequently used proteolytic enzyme in protein structure analysis.…”

“…The factors that result in the proline effect have been investigated over the past two decades . Attention was first focused on the unique structure of proline as it was the only amino acid found in mammalian proteins that contained a secondary amine .…”

“…Proton mobility was another factor which was considered determining the significance of the proline effect. By investigating the tandem mass spectra of over 130,000 proline‐containing peptides in NIST Libraries, Dong et al suggested that the selective cleavage at N‐terminal side of Pro was suppressed when all protons were nonmobile . Breci and coworkers analyzed the fragmentation data of doubly charged peptides in database, and concluded that the side chain of the adjacent residue to Pro played a role in the cleavage of the Xxx‐Pro bond via restricting the conformation of the proline‐containing peptides .…”

High-energy electron transfer dissociation of protonated amino acids

“…For structure analysis of the gaseous ions including the protonated molecules, collisionally activated dissociation (CAD) has been used as a traditional method in various tandem mass spectrometers (MS/MS) [4] on the market. The disadvantages of CAD, which does not provide comprehensive backbone cleavage for the protein and peptide, especially when they include the proline residue [5,6], and does not provide the position of the post translational group [7], have been overcome by electron capture dissociation (ECD) [8] equipped in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) and electron transfer dissociation (ETD) [9,10] equipped in an ion trap mass spectrometer. ETD of protonated peptides and proteins is rich and diverse for sequence elucidation, especially for determining the position of the posttranslational modification.…”