ESI-MS Fragmentation Pathways of N-Methylpyrrole Polyamide/Peptide Conjugates

MS/MS fragmentation pathways of polyamide/peptide conjugates, which are synthetic analogues of natural products with DNA affinity are discussed. The main fragmentation pathways involve the cleavage of the C-CO between rings and carbonyl groups, CO-NH amide bonds and NH-C bond between the NH groups and the ring. The fragment ions at M-100⁺ in the MS/MS spectra of the M+H⁺ ions of compounds prove the compound containing his group. If the MS/MS spectra of a compound shows characteristic M-100⁺ ions and M-137⁺ ions, that means this compound has a histidine containing Boc group.