Overview of the ALEX software framework and auxiliary workflow.

The ALEX framework comprises six core modules (grey colored boxes). The function of each module is explained in the Results and Discussion section. The output of the ALEX framework includes a data file with identified lipid species, intensities and accessory lipid features across all processed samples and FT MS scan ranges. The ALEX output is organized in database table format that can be accessed and processed by the auxiliary workflow using Orange and Tableau software. The auxiliary workflow is designed to integrate sample information, compute lipid molar abundance, implement quality control procedures and visualize lipidome data.