Prediction of fragmentation pathway of natural products, antibiotics, and pesticides by ChemFrag

Because the manual interpretation of ESI-MSn fragmentation spectra is time-consuming and usually requires expert knowledge, automated annotation is often sought. The fragmentation software ChemFrag enables the annotation of MSn spectra by combining a rule-based fragmentation and a semiempirical quantum chemical approach. In this study, the rule set was extended by 31 cleavage rules and 12 rearrangement rules and used for the interpretation of ESI(+)-MSn spectra of antibiotics, pesticides, and natural products as well as their structural analogs. The fragmentation pathways predicted by ChemFrag for compounds such as 17β-estradiol were confirmed by a comparison with pathways published in other studies. In addition, the annotations were compared with those of the programs MetFrag and CFM-ID, for example, with regard to the number and intensity of annotated fragment ions. Our experiments show that ChemFrag provides reliable and in some cases chemically more realistic annotations for the fragment ions of the investigated compounds. Thus, ChemFrag is a helpful addition to the established in silico methods for the interpretation of ESI(+)-MSn spectra.