Chlorophyllins are components of green food colorants and coloring foodstuff. However, in spite of its common consumption, the knowledge regarding these compounds is scarce, among other factors due to the complexity of identification. It is frequent to find groups of 2-4 chlorophyll derivatives, potentially present in green natural food colorants, with the same elemental composition, but different functional groups. This significantly increases the difficulty of correct identification, while the unintended misidentification is likely if the occurrence of structural isomers is not noted. We made use of data-dependent MS2 experiments on individual molecular ions to identify new chlorophyll derivatives, which structural arrangement was predictable on the basis of the chemical reactions taking place during the production of food green colorants; to provide qualifier ions by which structural isomers that differ at the sort of branched functional group(s), arising after the hydrolysis of the isocyclic ring, can be distinguished; and to increase our knowledge in chemical behavior of chlorophyll derivatives during MS experiments. To the best of our knowledge, there is no current existing proposal to discern among structural isomers of chlorophyll derivatives present in marketed green food colorants and coloring foodstuff products. The data we compiled showed the identification of qualifier ions to distinguish among structural isomers of non-coppered chlorophylls. In addition, taking advantage of the capacity of the powerful post-processing software, the fragmentation patterns and structural configuration of each qualifier ions are also ascertained.