One of the students in the first session of our class, John Cloutier, provided the following example that illustrates how CyclopeptideSequencing works. Consider a strange amino acid alphabet consisting of just two amino acids with masses 1 and 3. The figure below shows the peptides generated at each step by CyclopeptideSequencing with respect to a sample experimental spectrum {0, 1, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 5, 6}. Consistent peptides are shown in black, and inconsistent peptides are shown in red. In step 4, CyclopeptideSequencing produces the blue peptides 1-1-1-3, 1-1-3-1, 1-3-1-1, and 3-1-1-1; these four linear peptides all represent the same cyclic peptide, whose spectrum is equal to the experimental spectrum.

For example book suggests that glycine has elemental composition C2H3ON (integer mass 24+3+16+14=57 Da), whereas Wikipedia suggests that it is C2H5ON2 (integer mass 24+5+16+28=75 Da). We should use the former formula in analyzing mass spectra, since when an amino acid forms a peptide bond, it loses a water molecule (H2O).