Architecture of LipidXplorer. Boxes represent functional modules and arrows represent data flow between the modules. The import module converts technical replicates (collections of MS and MS/MS spectra) into a flat file database termed the MasterScan (.sc). Then the interpretation module probes the MasterScan with interpretation queries written in molecular fragmentation query language (MFQL). Finally, the output module exports the findings in a user-defined format. All LipidXplorer settings (irrespective of what particular module they apply to) are controlled via a single graphical user interface.