Determination of the primary structure of peptides using fast atom bombardment mass spectrometry

The determination of the amino acid composition and sequence of a peptide, using both conventional and tandem fast atom bombardment mass spectrometry, is presented. First a list of potential empirical formulae is generated using the accurate mass and isotopic peak intensity ratios from the molecular ion cluster. The formulae are mathematically analyzed to ensure that they correspond to linear peptides composed of 19 common amino acids. Then using the ions below m/z 160 Da, which are characteristic of the amino acid content of the peptide, the formulae are decomposed into possible amino acid compositions. From each composition sequences are generated and their predicted fragment ions are compared to ions present in the mass spectrum. A score based on the intensities and the occurrence of consecutive sequence fragments is calculated. Finally sequences with the ten highest scores are retained. Analyses performed on typical peptides with molecular weights below 1500 Da indicate that identification can generally be achieved using this approach.