Peptides: Chemistry and Biology, 2nd Edition by Norbert Sewald, Hans-Dieter Jakubke

By Norbert Sewald, Hans-Dieter Jakubke

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J31 j 2 Fundamental Chemical and Structural Principles 32 Coupling to high-performance separation techniques allows quantitation. MS/MS is a suitable method for the sequence analysis of a peptide, and is proving indispensable for proteome analysis. Peptides are prone to fragment at amide bonds after lowenergy collisions, resulting in a predictable fragmentation pattern. Consequently, sequence information can be obtained by this technique because most amino acids have unique masses. Only the pairs of Leu/Ile and Lys/Gln cannot be distinguished.

It could be demonstrated that the 20 common proteinogenic amino acid residues are compatible with this technique, but only up to eight residues of C-terminal sequences can be determined. MALDI instruments with delayed extraction [100, 101] allow the discrimination of all amino acids except Leu and Ile. Lys and Gln, having the same mass, can be distinguished after chemical acetylation with the formation of N e-acetyllysine. 9 Assignment of Disulfide Bonds and Peptide Fragment Ordering In order to determine disulfide bond positions present in a peptide or protein, the latter is hydrolyzed under conditions such that the risk of disulfide exchange is minimized.

5 N-Terminal Sequence Analysis (Edman Degradation) The most efficient method for stepwise degradation of a peptide chain starting from the N-terminus was developed by Pehr Edman in 1949 [71]. This cyclic process consists of three steps: coupling, degradation, and conversion. 14). Extractive removal of excess PITC is followed by treatment with an anhydrous strong acid such as trifluoroacetic acid to cleave the N-terminal amino acid to give its 2-anilino-5(4H)-thiazolone derivative, without attacking the rest of the peptide bonds within the chain.

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