Peptide Sequencing and Proteomics

Only the peptide subunits of a protein can be efficiently fragmented by CID for tandem MS analysis. Identifying a protein from such a peptide jumble is called bottom-up protein analysis. The corresponding tandem MS of the entire protein 

Note Examples and mechanistic aspects of peptide fragmentation are also covered in the context of tandem MS (see Chaps. 9.6.6, 9.8, and 9.10.1). The mechanism of peptide cleavage upon ECD is discussed in Chap. 9.13.2 with an exanple in Chap. 9.14.4 peptide ETD spectra are given in Chap. 9.15. Some further examples will follow in Chap. 12. 

The base fragment ion series due to amide bond cleavages are formed by b-ions on the N-terminus and y-ions on the C-terminus. The signals of the a-ions are set off to lower mass by 28 u (CO loss) from the b-ions, while c-ions are 17 u (NH3) heavier than b-ions as the adjacent N-C bond is cleaved. The x-ions of the C-terminal series are by 26 u lighter than y-ions (minus CO, plus H2) and z-ions are again by 17 u (NH3) heavier than y-ions. 

Note Peptides show marked differences, though having a great deal in common. Biochemists always emphasize the enormous variability of peptides and proteins assembled from as just twenty amino acids and the plethora of resulting functional characteristics. Accordingly, one should stay aware of the fact, that every (peptide) molecule has intrinsic properties also determining their fragmentation into ions. 

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