Amides, Peptides and Proteins

Mass spectrometry is one of the major techniques in the interdisciplinary field of proteomics. It provides a rapid, sensitive and reliable means of protein identification and structural determination, allowing for development in this newly baptised but yet classical field of biochemistry and biomedicine. The use of electrospray ionisation in conjunction with a tandem mass spectrometer (MS/MS) provides essential amino acid sequence information from the m/z values of the so-called b andy ions formed from cleavage of the amide bond of a protonated peptide. This reaction requires proton catalysis, and the mechanism is of interest in the present context, since it is closely related to the processes occurring in other protonated carboxylic acid derivatives. 

The simplest model of an amide bond is found in formamide, and several features of protonated formamide are highly relevant to the cleavage of protonated peptides into b and y ions. Amides are bidentate bases, and it has been demonstrated from correlations between core electron energies and proton affinities [213] and from quantum chemical calculations [214] that the carbonyl oxygen is more basic than the amide nitrogen. As demonstrated by FT-ICR, metastable ion dissociation, and RRKM and quantum chemical model calculations [214], the unimolecular dissociation of a protonated formamide molecule depends on which site the proton is attached to  

A critical reader would perhaps note that the proton affinities of the individual amino acids are not directly relevant to peptides, since the basic amino groups of amino acid are incorporated in amide bonds, for which the nitrogen basicity is far lower. For whole peptides or proteins, even more basic sites are found at the termini of side chains, as in the cases of lysine, histidine and arginine. However, as we will see below, the basicity of the free amino group created during peptide bond dissociation is crucial in determining which of the two dissociation products that will end up with the transferable proton, and thereby the charge. 

The fragmentation of protonated amino acids was the subject of several early investigations [238-240]. The most pronounced reaction is loss of the elements C02H2. Detailed quantum chemical calculations of the potential energy hypersurface of protonated glycine demonstrated that the sequence of events preceding this dissociation are [231,241,242]  

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S. Macholl, D. Tietze and G. Buntkowsky, NMR Crystallography of Amides, Peptides and Protein-Ligand Complexes, CrystEngComm, 2013, 15, 8627. 

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