Protonated peptides, fragmentation

Protonated peptides fragment in ways that are now well established (Fig. 11.8). Note that the "a," "b," and "c" ions incorporate the peptide s N-terminus, while "x," "y," and z" ions incorporate the peptide s C-terminus. The numerical subscript refers to the number of residues that the ion contains, "c" and "y" ions involve rearrangements that add to the ions two more hydrogens than they would have from simple cleavage alone. Figure 11.9 shows the CID spectrum of the protonated molecular ion... 

UV/Visible Photodissociation. In the case of UV/visible PD the photon energies are high enough to enable direct fragmentation. Previously, UV photodissociation was utilized mainly to study dissociation kinetics of gas-phase ions, but recently it was demonstrated that UV PD could be used for tandem MS of MALDI generated protonated peptides [18]. 

Dongre, A.R. Somogyi, A. Wysocki, V.H. SID an Effective Tool to Probe Structure, Energetics and Fragmentation Mecharrisrrrs of Protonated Peptides. J. Mass Spectrom. 1996, 31, 339-350. 

Scheme 1 The Expected Fragmentation Pattern of Protonated Peptide Ions and the Nomenclature of the Amino Acid Sequence Fragment Ions for Determining Amino Acid Sequences...

ECD has recently been introduced as an alternative activation method to obtain fragmentation of multiply protonated peptides [57]. An example of an ECD fragmentation spectrum... 

Fragmentation paths yielding the c and z ions after activation of a multiply protonated peptide by ECD. 

Fragment ion spectrum of a protonated peptide and (top) the sequence of ions. 

Fig. 7. The mechanism for formation of b andy ions during fragmentation of protonated peptides and protein. The mass spectral pattern of b and y ions are used to determine the amino acid sequence...

Paizs B, Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005 24 508-548. 

Scheme 4 Synthesis of the Peptide Fragment 9-14 of Somatostatin-28 Using the Protonated Arginine Approach ...

From these databases, the atomic coordinates of fragments of three amino-acids matching the Xaa-Pro-Aro(0 sequence motif were extracted (t = index number of the aromatic residue). The sequences of the residue peptide fragments found in this way were mutated to Gly-Pro-Phe, in order to make comparison possible. For each peptide, the main-chain and side-chain dihedral angles, (J) / co Xjj, and all the proton chemical shifts were computed. Finally, the structures were clustered according to their backbone conformations and their computed chemical shifts. 

It should be noted that ETD is a relatively inefficient process for doubly protonated peptide precursors [M + 2H]2+, which are the ions most commonly found in bottom-up proteomics experiments. This situation may be retrieved, however, by using a supplemental low-energy CID method (ETciD) to target the nondissociated electron transfer (ET) product, [M + 2H]2+. CID of the ET product then yields c- and z-type fragment ions. Swaney etal.110 have reported that in a large-scale analysis of doubly charged tryptic peptides, the use of ETciD resulted in a median sequence coverage of 89% compared to 63 and 77% for ETD and CID, respectively. 

Cr (CO)6 and protonated peptide surface induced dissociation (SID) AMI Shattering fragmentation, apparent non-RRKM dynamics [123-125]... 

Modem mass spectrometric methods greatly help to speed up degradation studies by identifying the molecular mass of peptide fragments. Various desorption techniques, which produce protonated protein ions in the gas phase, are applied. Prominent examples are fast-atom bombardment (FAB) and matrix- assisted laser desorption/ionization (MALDI). Most commonly these techniques provide only the mass of the molecular ion, but they can be coupled with a collision-induced dissociation (CID) procedure. The ions are activated by collisions with neutral target gases, and the peptides dissociate in the gas phase. The resulting mass spectra... 

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