Organization of a MasterScan file. LipidXplorer imports and aligns MS and MS/MS spectra into a flat file database MasterScan. It is shown here as a file cabinet addressed at the top-level by precursor masses in the MS spectrum, while their intensities are assigned to individual acquisitions. In this example the lipid precursor with m/z 788.55 was observed in all acquisitions with an intensity (in arbitrary units) of 203745 in Acquisition 1; 120668 in the Acquisition 2; ... till 35746 in Acquisition n. This precursor m/z 788.55 was fragmented in each acquisition. Masses of fragments were aligned and substituted by the averaged representative masses, while the intensities of corresponding peaks in each individual acquisition were stored. For example, the fragment with m/z 184.07 has an intensity of 181716 in Acquisition 1; 104364 in Acquisition 2; ..., till 27854 in Acquisition n.