Evaluation of gas chromatography-atmospheric pressure chemical ionization-mass spectrometry as an alternative to gas chromatography-electron ionization-mass spectrometry: Avocado fruit as example

•Development of GC-APCI-MS and GC-EI-MS methods for metabolic profiling of avocado fruit.•First application of a very recently developed GC-APCI database.•A total of 100 compounds were identified in avocado fruit extracts.•MS signals observed in both ionization sources has been compared.

Although GC-APCI-MS was developed more than 40 years ago this coupling is still far from being a routine technique. One of the reasons explaining the limited use of GC-APCI so far is the lack of spectral database which facilitates the identification of the compounds under study. The first application of a very recently developed GC-APCI database to identify as many compounds as possible in a complex matrix such as avocado fruit is presented here. The results achieved by using this database has been checked against those obtained using traditional GC-EI-MS and a comparison of the MS signals observed in both ionization sources has been carried out. 100 compounds belonging to different chemical families were identified in the matrix under study. Considering the results of this study, the wide range of application (in terms of polarity and size of analytes) and the robustness of APCI as interface, the high quality of TOF spectra, and our library as a publicly available resource, GC-APCI-TOF MS is definitively a valuable addition to the “metabolomics toolbox”.