Tandem mass spectrometry for the structural determination of backbone-modified peptides

A variety of backbone-modified peptides were desorbed by fast atom bombardment and collisionally activated. These peptide modifications involve the replacement of a normal [CONH] peptide linkage with such groups as thiomethylene ether (CH2S), thioamide (CSNH), methyleneamine (CH2NH), and thiomethylene sulfoxide (CH2SO) moieties. Modified linear peptides decompose to give fragmentations characteristic of the modifications as well as typical peptide bond fragments. The presence of a replacement group in cyclic peptides can induce new fragmentations. The presence of other functional groups, such as an exocyclic N-terminal residue, however, can dominate the observed fragmentations. Upon collisional activation, unmodified linear peptides fragment to give N-terminal ions as the most abundant daughter ions. In comparison, ψ[CH2NH] and ψ[CH2S ] modified linear peptides decompose to give prominent C-terminal sequence ions. The ψ[CH2SO] modified linear peptides, however, fragment into both N- and C-terminal ions of high relative abundance. Depending on the modification, daughter ions or internal fragment ions are observed that are characteristic of the amide bond replacement. Useful structural information can therefore be obtained.