Sequence-specific fragmentation

Brown, R. S. Lennon, J. J. Sequence-specific fragmentation of matrix-assisted laser-desorbed protein/peptide ions. Anal. Chem. 1995,67,3990-3999. 

One proposal to increase the visibility of the b and y sequence-specific ions and to provide complete sequence information is to derivatize phosphopeptides.106 Sequence analysis can also be improved by using the /3-elimination chemistry.102,107 As described above in this section, phosphoserine and phosphothreonine can be converted to S-ethylcysteine and 5-ethyl-/3-methylcysteine, respectively, upon the base-catalyzed /3-elimination of the phosphate group, followed by the reaction with ethanethiol. CID of the modified peptides results in more evenly distributed sequence-specific fragment ions. 

Lee, H. and Lubman, D. M., Sequence-Specific Fragmentation Generated by Matrix-Assisted Laser Desorption/Ionization in a Quadrupole Ion Trap/Re-flectron Time-of-Elight Device, Anal. Chem., 67, 1400, 1995. 

Two methods are used to sequence MALDI-produced ions by TOFMS One approach uses ion-source decay, sequence ions thus produced are characterized by operating the TOF instrument in the delayed-extraction mode. Fast dissociation in the source-accelerating region creates a wealth of sequence-specific fragment ions, which otherwise would be missed in the normal mode of operation of TOF (i.e., in which the laser pulse and ion-extraction pulse are both applied concurrently). By applying a delayed-extraction pulse, fragments can, however, be accumulated between pulses and mass-analyzed with an ordinary linear TOFMS instrument [98,99]. This process preferentially forms c -type N-terminus ions along with y and C-terminus ions. Similar to FAB and ESI in-source CID, this approach requires a pure sample and is not applicable to a mixture of peptides. 

Several gas-phase sequencing techniques have attained success all rely on the generation and mass analysis of sequence-specific fragment ions [38-40], These methods have the advantage of simplicity and are potentially faster than solution-phase methods. 

Fragmentation of Protonated Peptides. The amino acid sequence-specific fragmentation of peptides is directed by the site of protonation. For peptides containing arginine and lysine, protonation occurs primarily on these basic residues. However, in order to anticipate the entire set of possible protonated fragments that may be... 

FIGURE 11.23 Notation for the formation of sequence-specific fragment ions for oligonucleotides. (Reprinted with permission from reference 24). 

ScHULTEN, H.-R., and H. M. Schiebel Sequence Specific Fragments in the Field Desorption Mass Spectra of Dinucleoside Phosphates. Nucleic Acids Res. 3, 2027 (1976). 

Lee, H. Lubman, D. M. Sequence-specific fragmentation generated by matrix-assisted laser desorption/ionization in a quadrupole ion trap/ reflectron time-of-flight device. Anal. Chem. 1995,... 

---