Fragmentation of Peptides

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.

Figure 20. Chromatographic separation of thermolytic fragments of peptide T-9 isolated from the tryptic digest of the AE-p-chain of Hl Sheperds Bush. The Dowex 1-X2 column uxis 60 cm long and had an internal diameter of 0.6 cm. The pH gradient is indicated by the broken line. The fragments are identified bu their sequences and the positions they occupy in the p-chain. The sequence of the abnormal T-9 is given at the top of the figure.

Mass spectrometry not only allows the precise determination of the molecular mass of peptides and proteins but also the determination of their sequences, especially when used with tandem mass techniques. Indeed, fragmentation of peptides and proteins gives sequence information that can be used for protein identification, de novo sequencing, and identification and localization of post-translational or other covalent modifications [ 17-24]. 

Structure and Sequence Determination Using Fragmentation 8.2.2.1 Fragmentation of Peptides... 

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. 

Watlenberg, A.,Oigan, A.J., Schneider, K., Tyldesley, R., Bordoli, R. and Bateman, R.H. (2002) Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) Mass spectrometry and its implications for protein identification. J. Am. Soc. Mass Spectrom. 13, 772-783. 

Figure 4 Protected fragments of peptide and synthesis scheme for GIP.

Analysis of the linear strain in crystalline amino acids, in particular - the analysis of the compressibility of selected structural elements - molecular chains, layers, intermolecular hydrogen bonds, voids - is important for an understanding of the compressibilities of structural fragments of peptides and proteins - helices, sheets, turns, non-structured fragments and cavities. For example, in proteins loops are often more compressible than helices, which are in turn more compressible than / -sheets [9, 88, 107, 108, 110, 192, 193]. The compressibility of main chains is comparable with the strain in crystalline amino acids. This comparison should... 

P. Stefanowicz, K. Kapczyhska, M. Jaremko, L. Jaremko, and Z. Szewczuk, A mechanistic study on the fragmentation of peptide-derived Amadori products, J. Mass Spectrom., 44 (2009) 1500-1508. 

At this point we would also like to mention a versatile tool to model mass spectra and mass fragmentation spectra in silico. A range of proteomics tools is combined in MassXpert, a free application by F. Rusconi, which can be downloaded from http //frl.lptc.u-bordeaux.fr). Supported features include cleavage of a protein by different enzymes, fragmentation of peptides or small proteins, an m/z calculator for a given protein mass and many more. 

Steen, H. Mann, M. Similarity between condensed phase and gas phase chemistry fragmentation of peptides containing oxidized cysteine residues and its implications for proteomics. /. Am. Soc. Mass Spectmm. 2001,12, 228-232. 

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