Fragmentation methods peptide ions

Figure 5.12 Structures and nomenclature of the ions formed in the mass spectral fragmentation of peptides which involve scission of the polypeptide backbone. From Chapman, J. R. (Ed.), Protein and Peptide Analysis by Mass Spectrometry, Methods in Molecular Biology, Vol. 61, 1996. Reproduced by permission of Humana Press, Inc.

The fragmentation of peptides can also be obtained by FTICR instruments. Besides the most commonly used activation method, namely CID, the activation can alternatively be performed without gas by infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD). These methods fragment peptide ions in the ICR cell by emitting a laser beam or electron beam, respectively. 

Fragmentation of peptides can also be observed with FTICR instruments. Infrared multiple photon dissociation (IRMPD) and electron capture dissociation (ECD) have been introduced as two alternative dissociation methods to the low-energy CID method. The IRMPD method produces many fragments that make the spectrum very complex and difficult to interpret. Some of the fragment types observed with IRMPD are b and y type ions or these ions that have lost ammonia or water. However, most of them are not these types of fragment ions. 

The distinction between these two peptides can also be performed at low energy by fragmenting the immonium ions from these amino acids at m/z 86. However, this method can be applied only to peptides that contain either leucines or isoleucines [63], Differentiation... 

Chapter 5 provides an overview of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and its applications in the structural characterization of peptides and proteins. The principles of FT-ICR, that is, ion motion, ion excitation/ detection, and instrumental considerations, are discussed and an explanation of the features of FT-ICR that make it so suitable for peptide/protein analysis is presented. New methods for the fragmentation of peptide and protein ions in FT-ICR mass spectrometry, such as sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD), blackbody infrared radiative dissociation (BIRD), surface-induced dissociation (SID), and electron capture dissociation (BCD), are described in detail. Innovative hybrid FT-ICR instruments, which have recently become available, are reviewed. In conclusion, the chapter discusses the applications of FT-ICR in bottom-up and top-down proteomics. 

Additional techniques can provide further information when the structure of a peptide is unknown. One method is to carry out the protein digestion in water that is labeled with 50% 0, yielding an isotopically labeled ( 0/ 0) doublet for every cleaved peptide. When such peptides are fragmented the y ions (and other C-terminal ions) can be readily identified, as each will retain the doublet, whereas the N-terminal fragments will have normal isotope distributions that contain only the isotope. 

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