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. https://static.wixstatic.com/media/undefined

For example book suggests that glycine has elemental composition C2H3ON (integer mass 24+3+16+14=57 Da), whereas Wikipedia (https://en.wikipedia.org/wiki/Glycine)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).