Peptides fragmentation nomenclature

For example, in the mass spectrum shown in Fig. 6.4, the mass difference between ions at 387.2 and 500.3 m/z is equal to 113.1, which suggests that they differ by Leu or He. Going to the right, 572.5 500.3 = 72.2, which corresponds to Ala, etc. It is often 

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FiGURE4.10 Peptide fragmentation nomenclature for ions produced from collision-induced dissociation of the peptide WEIN. The arrowheads show the fragments that retain the charge. The chemical formulas for the hj and ions are noted and the respective masses for the y- and h-ion series are listed for the tetrapeptide WEIN. 

No tandem MS experiment can be successful if the precursor ions fail to fragment (at the right time and place). The ion activation step is crucial to the experiment and ultimately defines what types of products result. Hence, the ion activation method that is appropriate for a specific application depends on the MS instrument configuration as well as on the analyzed compounds and the structural information that is wanted. Various, more or less complementary, ion activation methods have been developed during the history of tandem MS. Below we give brief descriptions of several of these approaches. A more detailed description of peptide fragmentation mles and nomenclature is provided in Chapter 2. An excellent review of ion activation methods for tandem mass spectrometry is written by Sleno and Volmer, see Reference 12, and for a more detailed review on slow heating methods in tandem MS, see Reference 13. 

Cyclic peptides are analyzed less frequently then the linear ones but their sequencing and nomenclature are much more complicated. There is no generally accepted nomenclature scheme but we describe here the one proposed by Ngoka and Gross [4]. It takes account of Roepstorff-Fohlmann s and Biemann s conventions but introduces amendments to address cyclic peptide fragmentation. 

K. Biemann, Nomenclature for Peptide Fragment Ions. In Methods in Enzymology, Vol. 193, J. A. McCloskey (ed.), Elsevier Science and Technology, Orlando, FL, 1990, 886-888. 

Fig. 5. Fragmentation nomenclature of peptides. Bond breakages of all bonds of the peptide backbone have a systematic name (I). When fragmenting multiply charged peptide ions the peptide bond breaks preferentially since it is among the most labile bonds and only relatively low collision energies are involved (II).

Biemann K. (1990), Nomenclature for peptide fragments ions, Meth. Enzymol. 193, 886-887. 

Figure 2 Nomenclature of peptide fragmentation. The possible product ion series that arise by cleavages along the peptide backbone are a-, b-, and c-series (N-terminal) and x-, y-, and z-series (C-terminal). (The designation +2H denotes addition of two hydrogens that are transferred onto the structures depicted in the figure to form the corresponding singly charged y- or c- product ions (21)). Under low-energy CID, y- and b-ions usually predominate. The mass differences between adjacent ions of the same series can be used to deduce portions of the peptide sequence.

Figure 15.13. Nomenclature used for the more common fragments produced by CID peptide fragmentation. The b and y fragment families , that occur when the peptide bond is broken, are normally produced at higher concentration.

Biemann, K., 1990, Appendix 5. Nomenclature for peptide fragment ions (positive ions). Methods Enzymol. 193 886-887. 

Scheme 17.21. Nomenclature for peptide fragmentations. (Adapted with permission from Ref. 82.)...

Table 5.5 Nomenclature of the ions formed in the mass spectral fragmentation of polypeptides. 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 6.4. Fragmentation spectrum of a tryptic peptide obtained from bovine serum albumin. Peptide sequence LGEYGFQNALIVR, monoisotopic [M + H]+ = 1479.796, monoisotopic [M+2H]2+ =740.402. Upper panel full scan MS spectrum. Lower panel MS/MS spectrum of a doubly-charged ion at 740.7 m/z with a ladder of y ions, the distances between which correspond to amino acid residues (upper row of letters). A shorter series of b ions is also seen (lower row of letters). See Fig. 6.5 for description of nomenclature. Note the often observed phenomenon where multiply-charged ions lose the charge during fragmentation process and, therefore, have higher m/z values than the original parent ion.

Figure 6.5. Nomenclature of peptide ions resulting from backbone fragmentation.

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...

Peptides extracted from casein with N, N-dimethyl formamide have complex electrophoretic patterns identical to those of the fraction first prepared by Long and co-workers and called X-casein (El-Negoumy 1973). These peptides are identical electrophoretically to those released by the action of plasmin, which is present in fresh raw milk, upon asr casein (Aimutis and Eigel 1982). Two of these peptides have tryptic peptide maps and molecular weights identical to those of a pair of the peptides produced by plasmin degradation of asl-casein. These peptides appear to be fragments of a8l-casein which are present in milk as the result of plasmin proteolysis. More definitive information on their primary structure is needed before nomenclature for these fragments can be established. 

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