Fast atom bombardment and tandem mass spectrometry of synthetic nucleopeptides

Positive and negative ion fast atom bombardment (FAB) combined with tandem mass spectrometry (MS/MS) has been used to sequence four fully protected nucleopeptides. Protonated and deprotonated molecules and some structurally significant fragments, predominantly sodium cationized/decationized adducts, are observed. The tandem mass spectra of the protonated/deprotonated molecules help to identify (bidirectionally) the main building blocks and the sequence ions of the peptide part of the nucleopeptide components. It is found that the cleavage of the peptide-phosphate backbone mainly occurs due to 1,5-H shift from the side chain of the neighbouring amino acid to the oxygen of the phosphate. It is also observed that the number of amino acids present in the peptide part has a potential influence on the location of the cationization (Na+) which in turn influences the fragmentation pattern in the mass spectrometer.